UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) [X] ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended September 30, 2005 OR [ ] TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Commission file number 33-26115 PATRIOT TRANSPORTATION HOLDING, INC. (Exact name of registrant as specified in its charter) FLORIDA 59-2924957 State or other jurisdiction of (I.R.S. Employer incorporation or organization Identification No.) 1801 Art Museum Drive, Jacksonville, Florida 32207 (Address of principal executive offices) (Zip Code) Registrant's telephone number, including area code 904/396-5733 Securities registered pursuant to Section 12(b) of the Act: None Securities registered pursuant to Section 12(g) of the Act: Common Stock $.10 par value (Title of class) Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes No X Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or 15(d) of the Act. Yes No X Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes X No Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant's knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K. [ ] Indicate by check mark whether the registrant is an accelerated filer (as defined in Rule 12b-2 of the Act). Yes No X Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act). Yes No X The number of shares of the registrant's stock outstanding as of December 7, 2005 was 2,965,075. The aggregate market value of the shares of Common Stock held by non-affiliates of the registrant as of March 31, 2005, the last day of business of our most recently completed second fiscal quarter, was $62,301,572. Solely for purposes of this calculation, the registrant has assumed that all directors, officers and ten percent (10%) shareholders of the Company are affiliates of the registrant. Documents Incorporated by Reference Portions of the Patriot Transportation Holding, Inc. 2005 Annual Report to Shareholders are incorporated by reference in Parts I and II. Portions of the Patriot Transportation Holding, Inc. Proxy Statement which will be filed with the Securities and Exchange Commission not later than December 31, 2005 are incorporated by reference in Part III. PART I Item 1. BUSINESS. Patriot Transportation Holding, Inc., which was incorporated in Florida in 1988, and its subsidiaries (the "Company") are engaged in the transportation and real estate businesses. The Company has two business segments: transportation and real estate. Industry segment information is presented in Notes 3 and 12 to the consolidated financial statements included in the accompanying 2005 Annual Report to Shareholders and is incorporated herein by reference. The Company's transportation business is conducted through two wholly owned subsidiaries, Florida Rock & Tank Lines, Inc. ("Tank Lines"), and SunBelt Transport, Inc. ("SunBelt"). Tank Lines is a Southeastern U.S. based transportation company concentrating in the hauling of primarily petroleum related bulk liquids and dry bulk commodities by tank trailers. SunBelt serves the flatbed portion of the trucking industry primarily in the Southeastern U.S., hauling primarily construction materials. The Company's real estate activities are conducted through two wholly owned subsidiaries. Florida Rock Properties, Inc. ("Properties") and FRP Development Corp. ("Development"). Properties owns real estate of which a substantial portion is under mining royalty agreements or leased to Florida Rock Industries, Inc. ("FRI"), a related party. FRI accounted for approximately 30% of the Company's real estate revenues for Fiscal 2005. Properties also owns certain other real estate for investment. Development owns, manages and develops commercial warehouse/office rental properties near Baltimore, Maryland. Substantially all of the real estate operations are conducted within the Southeastern and Mid-Atlantic United States. Revenues from royalties and from a portion of the trucking operations are subject to factors affecting the level of general construction activity. A decrease in the level of general construction activity in any of the Company's market areas may have an adverse effect on such revenues and income derived therefrom. Transportation. Tank Lines is engaged in hauling primarily petroleum related bulk liquids and dry bulk commodities by tank trailers. SunBelt is engaged primarily in hauling building and construction materials on flatbed trailers. During Fiscal 2005, Tank Lines operated from terminals in Jacksonville, Orlando, Panama City, Pensacola, Port Everglades, Tampa and White Springs, Florida; Albany, Atlanta, Augusta, Bainbridge, Columbus, Dalton, Macon and Savannah, Georgia; Knoxville, Tennessee; Montgomery, Alabama; and Charlotte and Wilmington, North Carolina. Tank Lines has from two to six major tank truck competitors in each of its markets. SunBelt's flatbed fleet is based in Jacksonville and Tampa, Florida; Atlanta and Savannah, Georgia; South Pittsburg, Tennessee; and Mobile, Alabama, and hauls primarily building and construction materials in the Southeastern U.S. There are at least ten major competitors in SunBelt's market area and numerous small competitors in the various states served. At September 30, 2005, the Company operated and owned a fleet of approximately 604 trucks, and owned a fleet of approximately 917 trailers. The Company was committed at September 30, 2005 to purchase 26 trailers and 77 tractors and plans to continue its routine fleet replacement and modernization program during 2006. The transportation segment primarily serves customers in the petroleum and building and construction industries. Petroleum customers accounted for approximately 69% and building and construction customers accounted for approximately 31% of transportation segment revenues for the year ended September 30, 2005. The Company hauls construction aggregates, diesel fuel and cement for FRI. Revenues from services provided to FRI accounted for 1.1% of the transportation segment's revenues. Price, service, and location are the major factors which affect competition in the transportation segment within a given market. During Fiscal 2005, the transportation segment's ten largest customers accounted for approximately 44.2% of the transportation segment's revenue. One of these customers accounted for 11.4% of the transportation segment's revenue. The loss of any one of these customers could have an adverse effect on the Company's revenues and income. Real Estate. The Company's real estate and property development activities are conducted through wholly owned subsidiaries. The Company owns real estate in Florida, Georgia, Virginia, Maryland, Delaware and Washington, D.C. The real estate owned falls generally into one of three categories: (i) land and/or buildings leased under rental agreements or being developed for rental; (ii) construction aggregates properties with stone or sand and gravel deposits, substantially all of which is leased to FRI under mining royalty agreements, as to which the Company is paid a percentage of the revenues generated by the material mined and sold, or minimum royalties where there is no current, or only limited, mining activity; and, (iii) land that is being held for future appreciation or development. Additional information about the Company's real estate segment is contained under the caption "Real Estate" and in Notes 3 and 12 to the consolidated financial statements included in the accompanying 2005 Annual Report to Shareholders and is incorporated herein by reference. The Company's real estate strategy of developing high quality, flexible warehouse/office space continues to be successful as average occupancy for the fiscal year for buildings in service for more than 12 months was 88.0%. At September 30, 2005, 86.8% of the total warehouse/office portfolio of approximately 2.3 million square feet was leased. Price, location, rental space availability, flexibility of design, and property management services are the major factors that affect competition in the flexible warehouse/office rental market. The Company experiences considerable competition in all of its markets. Real estate revenues in Fiscal 2005 were divided approximately 66% from rentals on developed properties and 34% from mining royalties. FRI accounted for approximately 30% of total real estate revenues. Tenants of flexible warehouse/office properties are not concentrated in any one particular industry. During 2003 and 2004, a subsidiary of the Company sold several parcels of property to FRI, a related party. The properties were located in St. Mary's County, MD, Lake City, FL, Springfield, VA, and Miami, FL and the combined sales price was $31,464,000. See Notes 3 and 4 to the consolidated financial statements for more information. Restatement of Prior Financial Information. The Company restated its consolidated balance sheet as of September 30, 2004 and its consolidated statement of shareholders' equity for the year then ended. There were no differences related to corrections reported in the consolidated statements of income or cash flows for the year ended September 30, 2004. The Company also restated its consolidated statements of income, shareholders' equity and cash flows for the year ended September 30, 2003. In addition, the Company restated its quarterly results of operations for fiscal 2005. The restatement also affected periods prior to fiscal 2003 and those periods have been restated where presented. The restatement corrects our historical lease accounting practices. See Note 2 to the Consolidated Financial Statements included in the accompanying 2005 Annual Report to Shareholders for more information. We did not amend our previously filed Annual Reports on Form 10-K or Quarterly Reports on Form 10-Q for the restatement, and the financial statements and related financial information contained in such reports should no longer be relied upon. Environmental Matters. While the Company is affected by environmental regulations, such regulations are not expected to have a major effect on the Company's capital expenditures or operating results. Seasonality. The Company's business is subject to limited seasonality due to the cyclical nature of business of our customers, with revenues generally declining slightly during winter months. Employees. The Company employed 903 people in its transportation group, 18 people in its real estate group and 4 people in its corporate offices at September 30, 2005. EXECUTIVE OFFICERS OF THE COMPANY Name Age Office Position Since Edward L. Baker 70 Chairman of the Board May 3, 1989 John E. Anderson 60 President & Chief Feb. 17, 1989 Executive Officer David H. deVilliers, Jr. 54 Vice President of the Feb. 28, 1994 Company and President of the Company's Real Estate Group Ray M. VanLandingham 62 Vice President, Dec. 6, 2000 Treasurer, Secretary and Chief Financial Officer John D. Klopfenstein 42 Controller and Chief Feb. 16, 2005 Accounting Officer Terry S. Phipps 41 President of SunBelt April 5, 2004 Transport, Inc. Robert E. Sandlin 44 President of Florida March 1, 2003 Rock & Tank Lines, Inc. All of the above officers have been employed in their respective positions for the past five years except as follows: John D. Klopfenstein served as Director, Business Development and Planning of the Company, from June 1, 2003 to February 15, 2005, and as Manager, Corporate Development of the Company, from July 1, 1996 to May 31, 2003; Terry S. Phipps was a Vice President of SunBelt from May 2003 to April 2004, Mr. Phipps was employed with Coastal Transport, Inc. from 1990 to May 2003; and Robert E. Sandlin was a Vice President of Florida Rock & Tank Lines from 1993 until March 2003. John D. Baker II, who is the brother of Edward L. Baker, and Thompson S. Baker II, who is the son of Edward L. Baker, are on the Board of Directors of the Company. All executive officers of the Company are elected by the Board of Directors. Item 2. PROPERTIES. The Company's principal properties are located in Florida, Georgia, Virginia, Washington, D.C., Delaware and Maryland. Transportation Segment Properties. The Company has 21 sites for its trucking terminals in Alabama, Florida, Georgia, North Carolina, and Tennessee. The Company owns 13 of these sites and leases 8. Real Estate Segment Properties. Principal properties held by Real Estate segment are discussed below under the captions Developed Properties, Future Planned Development, Construction Aggregates Properties, and Other Properties. At September 30, 2005 certain developed real estate properties having a carrying value of $58,812,000 were pledged on long- term non-recourse notes with an outstanding principal balance totaling $50,900,000. In addition, certain other properties having a carrying value at September 30, 2005 of $714,000 were encumbered by $1,300,000 of industrial revenue bonds that are the liability of FRI. FRI has agreed to pay such debt when due (or sooner if FRI cancels its lease of such property), and further has agreed to indemnify and hold harmless the Company on account of such debt. Developed Properties. At September 30, 2005, the Company owned 10 parcels of land containing 404 usable acres in the Mid- Atlantic region of the United States as follows: 1) Hillside Business Park in Anne Arundel County, Maryland consists of 49 usable acres near the Baltimore-Washington International Airport. The Company plans to develop approximately 540,000 square feet of warehouse/office space on this site. Infrastructure work on the site is substantially completed and three buildings with a total of 419,980 square feet are completed and leased, each to a single tenant. Current plans are to construct an additional 80,000 square feet of warehouse/office space in late fiscal 2006. 2) Lakeside Business Park in Harford County, Maryland consists of 83 usable acres. Seven warehouse/office buildings, totaling 671,550 square feet, have been constructed and are 94% leased. The remaining 31 acres are available for future development and will have the potential to offer an additional 485,000 square feet of comparable product. 3) 6920 Tudsbury Road in Baltimore County, Maryland contains 5.3 acres with 86,100 square feet of warehouse/office space that is 100% leased. 4) 8620 Dorsey Run Road in Howard County, Maryland contains 5.8 acres with 84,600 square feet of warehouse/office space. The lessee at Dorsey Run vacated the premises at the end of its lease term on December 31, 2004. An agreement has been executed to lease 40,000 square feet to commence on January 1, 2006. 5) Rossville Business Center in Baltimore County, Maryland contains approximately 10 acres with 190,517 square feet of warehouse/office space and is 87% leased. 6) 34 Loveton Circle in suburban Baltimore County, Maryland contains 8.5 acres with 29,722 square feet of office space, which is 100% leased. The Company occupies 24% of the space and 23% is leased to FRI's subsidiary Arundel. 7) Oregon Business Center in Anne Arundel County, Maryland contains approximately 17 acres with 195,615 square feet of warehouse/office space, which is 92% leased. 8) Arundel Business Center in Howard County, Maryland contains approximately 11 acres with 162,796 square feet of warehouse/office space, which is 71% leased. 9) 100-400 Interchange Boulevard in New Castle County, Delaware contains approximately 17 acres with 303,006 square feet of warehouse/office space, which is 68% leased. 10) 1187 Azalea Garden Road in Norfolk, Virginia contains approximately 12 acres with 188,093 square feet of warehouse/office space, which is 100% leased. Future Planned Developments. Bird River, located in southeastern Baltimore County, Maryland, is a 179-acre tract of land that will have direct access to Maryland State Road 43 which is under construction and will connect I-95 with Martin State Airport. This property is currently zoned for residential and commercial use with 104 developable acres. The Company plans to develop and lease approximately 515,000 square feet of multiple warehouse/office buildings on the 42 developable acres zoned for commercial use. A subsidiary of the Company has entered into an agreement to develop and sell to a major national homebuilder a minimum of 292 residential lots on the residential portion of the Bird River Property. The agreement is subject to a number of contingencies, including (i) the approval by Baltimore County of a Planned Unit Development (PUD) by July 1, 2006 allowing the development of a minimum of 292 residential lots, (ii) the construction of Route 43, (iii) vehicular, water and sewer connection access to the property by July 1, 2007 at what the subsidiary deems to be a commercially reasonable cost, and (iv) other customary conditions precedent. Assuming that these conditions are satisfied and the development proceeds, the agreement provides for a minimum aggregate purchase price for these lots of $28,705,000. Patriot owns approximately 3,443 acres of land near Brooksville, Florida that it leases to FRI under a long-term mining lease. FRI also owns approximately 553 acres of land in Brooksville. Patriot and FRI management believe that FRI and Patriot may possibly realize greater value from the Brooksville property through development rather than continued mining. Accordingly, the independent directors of Patriot and FRI are considering a proposal to form a 50-50 joint venture to develop the Brooksville property. If this proposal is approved, the joint venture development will move forward only if zoning and permitting approvals are obtained that permit development of the property in a manner acceptable to Patriot and FRI; otherwise, Patriot intends to continue to lease the property to FRI for mining and related purposes. If the development proceeds, FRI will continue to conduct mining operations on at least a portion of the property. The Company owns a 5.8 acre parcel of undeveloped real estate in the southeast quadrant of Washington, D.C. that fronts the Anacostia River and a nearby 2.1 acre tract on the same bank of the Anacostia River. Currently, these properties are leased to FRI on a month-to-month basis. For several years, the Real Estate Group has been pursuing development efforts with respect to the 5.8 acre parcel. The Company previously obtained a Planned Unit Development (PUD) Zoning approval for development of the property and has been working to obtain approval of a modified PUD that would allow up to 625,000 square feet of commercial development and up to 440,000 square feet of residential development. If the modified PUD is approved, the Company would have up to two years to commence development in accordance with the modified PUD. The development of this property is likely to be impacted, at least to some degree, by the proposed construction on nearby property of a new baseball stadium for the Washington Nationals baseball team. While the Company currently believes that the construction of this proposed stadium would be a positive development for the property, the Company cannot yet determine the potential impact on its development plans if the stadium is built at the proposed location. The Company will monitor ongoing developments relating to the stadium while continuing to pursue its existing plans to develop the property. The Company owns a 50-acre, rail accessible site on Commonwealth Avenue in Jacksonville, Florida near the western beltway of Interstate-295 capable of supporting approximately 500,000 square feet of eventual warehouse/office build-out. Construction Aggregates Properties. The following table summarizes the Company's principal construction aggregates locations and estimated reserves at September 30, 2005, substantially all of which are leased to FRI. Tons of Tons Sold Estimated in Year Reserves Ended at 9/30/05 9/30/05 Approximate (000's) (000's) Acres Owned The Company owns eleven locations currently being mined in Brooksville, Grandin, Gulf Hammock, Keuka, Newberry and Airgrove/ Lake County, Florida; Columbus, Macon, Forest Park and Tyrone, Georgia; and Manassas, Virginia. 9,690 488,643 17,135 The Company owns four locations not currently being mined in Ft. Myers, Marion County, Astatula/Lake County and Sandland/Polk County, Florida - 32,891 2,339 Other Properties. In addition to the development, mining and rental sites, the Company owns approximately 2,045 acres of investment and other real estate. The Company owns an office building with approximately 69,000 square feet situated on approximately 6 acres in Jacksonville, Florida, which is leased to FRI. Item 3. LEGAL PROCEEDINGS. Note 15 to the Consolidated Financial Statements included in the accompanying 2005 Annual Report to Shareholders is incorporated herein by reference. Item 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS. No reportable events. PART II Item 5. MARKET FOR REGISTRANT'S COMMON EQUITY, RELATED STOCKHOLDER MATTERS AND ISSUER PURCHASES OF EQUITY SECURITIES. There were approximately 679 holders of record of Patriot Transportation Holding, Inc. common stock, $.10 par value, as of September 30, 2005. The Company's common stock is traded on the Nasdaq Stock Market (Symbol PATR). Information concerning stock prices is included under the caption "Quarterly Results" on page 7 of the Company's 2005 Annual Report to Shareholders, and such information is incorporated herein by reference. The Company has not paid a cash dividend in the past and it is the present policy of the Board of Directors not to pay cash dividends. Information concerning restrictions on the payment of cash dividends is included in Note 5 to the consolidated financial statements included in the accompanying 2005 Annual Report to Shareholders and such information is incorporated herein by reference. Information regarding securities authorized for issuance under equity compensation plans is included in Item 12 of Part III of this Annual Report on Form 10-K and such information is incorporated herein by reference. Purchases of Equity Securities by the Issuer and Affiliated Purchasers (c) Total Number of Shares (d) Purchased Approximate (a) As Part of Dollar Value of Total (b) Publicly Shares that May Number of Average Announced Yet Be Purchased Shares Price Paid Plans or Under the Plans Period Purchased per Share Programs or Programs (1) July 1 through July 31 0 $ 0 0 $ 3,490,000 August 1 through August 31 0 $ 0 0 $ 3,490,000 September 1 through September 31 0 $ 0 0 $ 3,490,000 Total 0 $ 0 0 (1) In December, 2003, the Board of Directors authorized management to expend up to $6,000,000 to repurchase shares of the Company's common stock from time to time as opportunities arise. Item 6. SELECTED FINANCIAL DATA. Information required in response to this Item 6 is included under the caption "Five Year Summary" on page 6 of the Company's 2005 Annual Report to Shareholders and such information is incorporated herein by reference. Item 7. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATION. Information required in response to Item 7 is included under the caption "Management Analysis" on pages 8 through 12 of the Company's 2005 Annual Report to Shareholders and such information is incorporated herein by reference. Item 7.A QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK. The Company is exposed to market risk from changes in interest rates. For its cash and cash equivalents, a change in interest rates affects the amount of interest income that can be earned. For its debt instruments with variable interest rates, changes in interest rates affect the amount of interest expense incurred. The Company did not have any variable rate debt outstanding at September 30, 2005, so a sensitivity analysis was not performed to determine the impact of hypothetical changes in interest rates on the Company's results of operations and cash flows. The following table provides information about the Company's long-term debt (dollars in thousands): There Fair Liabilities: 2006 2007 2008 2009 2010 after Total Value Scheduled maturities of long-term debt: Fixed Rate $ 2,432 $2,584 $2,769 $2,968 $3,201 $36,946 $50,900 $52,976 Average interest rate 6.9% 6.9% 6.9% 6.9% 7.0% 7.0% Item 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA. Information required in response to this Item 8 is included under the caption "Quarterly Results" on page 7 and on pages 13 through 23 of the Company's 2005 Annual Report to Shareholders. Such information is incorporated herein by reference. Item 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND FINANCIAL DISCLOSURE. None. Item 9A. CONTROLS AND PROCEDURES. The Company maintains disclosure controls and procedures that are designed to ensure that information required to be disclosed in the Company's reports under the Securities Exchange Act of 1934, as amended (the "Exchange Act"), is recorded, processed, summarized and reported within the time periods specified in the SEC's rules and forms, and that such information is accumulated and communicated to management, including the Company's Chief Executive Officer ("CEO"), Chief Financial Officer ("CFO"), and Chief Accounting Officer ("CAO"), as appropriate, to allow timely decisions regarding required disclosure. The Company also maintains a system of internal accounting controls over financial reporting that are designed to provide reasonable assurance to the Company's management and Board of Directors regarding the preparation and fair presentation of published financial statements. All control systems, no matter how well designed, have inherent limitations. Therefore, even those systems determined to be effective can provide only reasonable assurance of achieving the desired control objectives. As of September 30, 2005, the Company, under the supervision and with the participation of the Company's management, including the CEO, CFO and CAO, carried out an evaluation of the effectiveness of the design and operation of the Company's disclosure controls and procedures. Based on this evaluation and subject to the disclosure below, the Company's CEO, CFO and CAO concluded that the Company's disclosure controls and procedures are effective in alerting them in a timely manner to material information required to be included in periodic SEC filings. In coming to the conclusion that our disclosure controls and procedures are effective, our management considered, among other things, the control deficiency related to our accounting for leases, which resulted in the need to restate our previously filed financial statements as disclosed in Note 2 to the consolidated financial statements included in the accompanying 2005 Annual Report to Shareholders. In this regard, our management reviewed and analyzed the Securities and Exchange Commission's Staff Accounting Bulletin ("SAB") No. 99, Materiality, Accounting Principles Board Opinion No. 28, Interim Financial Reporting paragraph 29 and SAB Topic 5-F, Accounting Changes Not Retroactively Applied Due to Immateriality. The CEO, CFO and CAO concluded that our disclosure controls and procedures were effective despite this deficiency because, among other reasons: (i) the restatement adjustments did not have a material impact on the financial statements of prior interim or annual periods taken as a whole; (ii) the cumulative impact of the restatement adjustments on shareholders' equity was not material on the financial statements of prior interim or annual periods; and (iii) we were required to restate our previously issued financial statements solely because the cumulative impact of the error, if recorded in the current period would have been material to the current year's reported net income. There have been no changes in the Company's internal controls over financial reporting during the fourth quarter that have materially affected, or are reasonably likely to materially affect, the Company's internal control over financial reporting. PART III Item 10. DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT. Information regarding the executive officers of the Company is set forth under the caption "Executive Officers of the Company" in Part I of this Form 10-K. Information concerning directors (including the disclosure regarding audit committee financial experts), required in response to this Item 10, is included under the captions "Election of Directors" and "Section 16(a) Beneficial Ownership Reporting Compliance" in the Company's Proxy Statement and such information is incorporated herein by reference. The Proxy Statement will be filed with the Securities and Exchange Commission not later than December 31, 2005. The Company has adopted a Financial Code of Ethical Conduct applicable to its principal executive officers, principal financial officers and principal accounting officers. A copy of this Financial Code of Ethical Conduct is filed as Exhibit 14 to this Form 10-K. Item 11. COMPENSATION COMMITTEE. Information required in response to this Item 11 is included under the captions "Executive Compensation," "Compensation Committee Report," "Compensation Committee," and "Shareholder Return Performance" in the Company's Proxy Statement and such information is incorporated herein by reference. The Proxy Statement will be filed with the Securities and Exchange Commission not later than December 31, 2005. Item 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT. Information required in response to this Item 12 is included under the captions "Common Stock Ownership of Certain Beneficial Owners" and "Common Stock Ownership by Directors and Officers" in the Company's Proxy Statement and such information is incorporated herein by reference. The Proxy Statement will be filed with the Securities and Exchange Commission not later than December 31, 2005. Equity Compensation Plan Information Number of Securities remaining available for Number of future Securities Weighted issuance to be Average under equity issued upon exercise compensation exercise of price of plans outstanding outstanding (excluding options, options, securities warrants warrants reflected in and rights and rights column (a)) Plan Category (a) (b) (c) Equity compensation plans approved by security holders 337,900 $30.72 109,700 Equity compensation plans not approved by security holders 0 0 0 Total 337,900 $30.72 109,700 Item 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS. Information required in response to this Item 13 is included under the caption "Related Party Transactions" in the Company's Proxy Statement and such information is incorporated herein by reference. The Proxy Statement will be filed with the Securities and Exchange Commission not later than December 31, 2005. Item 14. PRINCIPAL ACCOUNTING FEES AND SERVICES. Information required in response to this Item 14 is included under the caption "Independent Registered Certified Public Accounting Firm" in the Company's Proxy Statement and such information is incorporated herein by reference. The Proxy Statement will be filed with the Securities and Exchange Commission not later than December 31, 2005. PART IV Item 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES. (a) (1) and (2) Financial Statements and Financial Statement Schedules. The response to this item is submitted as a separate section. See Index to Financial Statements and Financial Statement Schedules on page 21 of this Form 10-K. (3) Exhibits. The response to this item is submitted as a separate section. See Exhibit Index on pages 18 through 20 of this Form 10-K. SIGNATURES Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized. Patriot Transportation Holding, Inc. Date: December 27, 2005 By JOHN E. ANDERSON John E. Anderson President and Chief Executive Officer (Principal Executive Officer) By RAY M. VAN LANDINGHAM Ray M. Van Landingham Vice President, Treasurer, Secretary and Chief Financial Officer (Principal Financial Officer) By JOHN D. KLOPFENSTEIN John D. Klopfenstein Controller and Chief Accounting Officer(Principal Accounting Officer) Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities indicated on December 27, 2005. JOHN E. ANDERSON LUKE E. FICHTHORN III John E. Anderson Luke E. Fichthorn III Director, President, and Chief Director Executive Officer (Principal Executive Officer) CHARLES E. COMMANDER III______ Charles E. Commander III RAY M. VAN LANDINGHAM Director Ray M. Van Landingham Vice President, Treasurer, Secretary and Chief Financial ROBERT H. PAUL III Officer(Principal Financial Officer) Robert H. Paul III Director JOHN D. KLOPFENSTEIN ____________ John D. Klopfenstein H. W. SHAD III_____ Controller and Chief Accounting H. W. Shad III Officer (Principal Accounting Officer) Director __________________ MARTIN E. STEIN, JR. Edward L. Baker Martin E. Stein, Jr. Chairman of the Board Director JOHN D. BAKER II_________________ JAMES H. WINSTON _________ John D. Baker II James H. Winston Director Director THOMPSON S. BAKER II_____________ Thompson S. Baker II Director PATRIOT TRANSPORTATION HOLDING, INC. FORM 10-K FOR THE FISCAL YEAR ENDED SEPTEMBER 30, 2005 EXHIBIT INDEX [Item 14(a)(3)] (3)(a)(1) Articles of Incorporation of Patriot Transportation Holding, Inc., incorporated by reference to the corresponding exhibit filed with Form S-4 dated December 13, 1988. File No. 33- 26115. (3)(a)(2) Amendment to the Articles of Incorporation of Patriot Transportation Holding, Inc. filed with the Secretary of State of Florida on February 19, 1991 incorporated by reference to the corresponding exhibit filed with Form 10-K for the fiscal year ended September 30, 1993. File No. 33- 26115. (3)(a)(3) Amendments to the Articles of Incorporation of Patriot Transportation Holding, Inc. filed with the Secretary of State of Florida on February 7, 1995, incorporated by reference to an appendix to the Company's Proxy Statement dated December 15, 1994. File No. 33-26115. (3)(a)(4) Amendment to the Articles of Incorporation of Patriot Transportation Holding, Inc., filed with the Florida Secretary of State on May 6, 1999 incorporated by reference to a form of such amendment filed as Exhibit 4 to the Company's Form 8-K dated May 5, 1999. File No. 33-26115. (3)(a)(5) Amendment to the Articles of Incorporation of Patriot Transportation Holding, Inc. filed with the Secretary of State of Florida on February 21, 2000, incorporated by reference to the corresponding exhibit filed with Form 10-Q for the quarter ended March 31, 2000. File No. 33-26115. (3)(a)(6) Amendments to the Articles of Incorporation of Patriot Transportation Holding, Inc. filed with the Secretary of State of State of Florida on February 7, 1995, incorporated by reference to an appendix to the Company's Proxy Statement dated December 15, 1994. File No. 33-26115. (3)(a)(7) Articles III, VII and XII of the Articles of Incorporation of Patriot Transportation Holding, Inc, incorporated by reference to an exhibit filed with Form S-4 dated December 13, 1988. And amended Article III, incorporated by reference to an exhibit filed with Form 10-K for the fiscal year ended September 30, 1993. And Articles XIII and XIV, incorporated by reference to an appendix filed with the Company's Proxy Statement dated December 15, 1994. File No. 33-26115. (3)(b)(1) Amended and Restated Bylaws of Patriot Transportation Holding, Inc. adopted August 3, 2005, incorporated by reference to Exhibit 3.1 to the Company's Form 8-K dated August 3, 2005. File No. 33-26115. (4)(a) Specimen stock certificate of Patriot Transportation Holding, Inc, incorporated by reference to an exhibit filed with Form S-4 dated December 13, 1988. File No. 33-26115. (4)(b) Rights Agreement, dated as May 5, 1999 between the Company and First Union National Bank, incorporated by reference to Exhibit 4 to the Company's Form 8-K dated May 5, 1999. File No. 33-26115. (10)(a) Various lease backs and mining royalty agreements with Florida Rock Industries, Inc., none of which are presently believed to be material individually, except for the Mining Lease Agreement dated September 1, 1986, between Florida Rock Industries Inc. and Florida Rock Properties, Inc., successor by merger to Grandin Land, Inc. (see Exhibit (10)(c)), but all of which may be material in the aggregate, incorporated by reference to an exhibit filed with Form S-4 dated December 13, 1988. File No. 33-26115. (10)(b) License Agreement, dated June 30, 1986, from Florida Rock Industries, Inc. to Florida Rock & Tank Lines, Inc. to use "Florida Rock" in corporate names, incorporated by reference to an exhibit filed with Form S-4 dated December 13, 1988. File No. 33-26115. (10)(c) Mining Lease Agreement, dated September 1, 1986, between Florida Rock Industries, Inc. and Florida Rock Properties, Inc., successor by merger to Grandin Land, Inc., incorporated by reference to an exhibit previously filed with Form S-4 dated December 13, 1988. File No. 33-26115. (10)(d) Summary of Medical Reimbursement Plan of Patriot Transportation Holding, Inc., incorporated by reference to an exhibit filed with Form 10-K for the fiscal year ended September 30, 1993. File No. 33-26115. (10)(e) Summary of Management Incentive Compensation Plans, incorporated by reference to an exhibit filed with Form 10-K for the fiscal year ended September 30, 1994. File No. 33- 26115. (10)(f) Management Security Agreements between the Company and certain officers, incorporated by reference to a form of agreement previously filed (as Exhibit (10)(I)) with Form S-4 dated December 13, 1988. File No. 33-26115. (10)(g)(1) Patriot Transportation Holding, Inc. 1995 Stock Option Plan, incorporated by reference to an appendix to the Company's Proxy Statement dated December 15, 1994. File No. 33-26115. (10)(g)(2) Patriot Transportation Holding, Inc. 2000 Stock Option Plan, incorporated by reference to an appendix to the Company's Proxy Statement dated December 15, 1999. File No. 33-26115. (10)(h) Agreement of Purchase and Sale dated October 21, 2003 between FRP Bird River, LLC and The Ryland Group, Inc., incorporated by reference to an exhibit filed with Form 10-K for the year ended September 30, 2003. File No. 33-26115. (10)(i) Amended and Restated Revolving Credit Agreement dated November 10, 2004 among Patriot Transportation Holding, Inc. as Borrower, the Lenders from time to time party hereto and Wachovia Bank, National Association as Administrative Agent, incorporated by reference to the Company's Form 8-K dated November 16, 2004. File No. 33-26115. (10)(j) The Company and its consolidated subsidiaries have other long-term debt agreements, none of which exceed 10% of the total consolidated assets of the Company and its subsidiaries, and the Company agrees to furnish copies of such agreements and constituent documents to the Commission upon request. (10)(k) Letter of Credit Facility between Patriot Transportation Holding, Inc. and SunTrust Bank, N.A. dated February 16, 2005, incorporated by reference to the Company's Form 8-K dated February 16, 2005. File No. 33-26115. (10)(l) Summary of compensation arrangements with non- employee directors, incorporated by reference to the corresponding exhibit filed with Form 8-K dated October 11, 2005. File No. 33-26115. 10)(m) Summary of compensation arrangements with Named Executive Officers, incorporated by reference to the corresponding exhibit filed with Form 10-Q for the quarter ended March 31, 2005. File No. 33-26115. (13) The Company's 2005 Annual Report to shareholders, portions of which are incorporated by reference in this Form 10-K. Those portions of the 2005 Annual Report to Shareholders which are not incorporated by reference shall not be deemed to be filed as part of this Form 10-K. (14) Financial Code of Ethical Conduct between the Company, Chief Executive Officers and Financial Managers, adopted December 4, 2002, incorporated by reference to an exhibit filed with Form 10-K for the year ended September 30, 2003. File No. 33-26115. (21) Subsidiaries of Registrant at September 30, 2005: Florida Rock & Tank Lines, Inc. (a Florida corporation); Florida Rock Properties, Inc. (a Florida corporation); FRP Development Corp. (a Maryland corporation); FRP Maryland, Inc. (a Maryland corporation); 34 Loveton Center LLC (a Maryland limited liability company); FRTL, Inc. (a Florida corporation); SunBelt Transport, Inc. (a Florida Corporation); Oz LLC(a Maryland limited liability company); 1502 Quarry, LLC(a Maryland limited liability company); FRP Lakeside LLC #1 (a Maryland limited company); FRP Lakeside LLC #2 (a Maryland limited liability company); FRP Lakeside LLC #3 (a Maryland limited liability company); FRP Lakeside LLC #4 (a Maryland limited liability company); FRP Lakeside LLC #5 (a Maryland limited liability company); FRP Hillside LLC (a Maryland limited liability company); FRP Hillside LLC #2 (a Maryland limited liability company); FRP Hillside LLC #3 (a Maryland limited liability company); FRP Windsor LLC (a Maryland limited liability company); FRP Dorsey LLC (a Maryland limited liability company); FRP Bird River LLC (a Maryland limited liability company); FRP Interchange LLC (a Maryland limited liability company); FRP Azalea LLC (a Maryland limited liability company). (23)(a) Consent of PricewaterhouseCoopers LLP, Independent Registered Certified Public Accounting Firm, appears on page 22 of this Form 10-K. (31)(a) Certification of John E. Anderson. (31)(b) Certification of Ray M. Van Landingham. (31)(c) Certification of John D. Klopfenstein. (32) Certification of Chief Executive Officer, Chief Financial Officer, and Chief Accounting Officer pursuant to 18 U.S.C. Section 1350, adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. PATRIOT TRANSPORTATION HOLDING, INC. INDEX TO FINANCIAL STATEMENTS AND FINANCIAL STATEMENT SCHEDULES (Item 15(a) (1) and 2)) Page Consolidated Financial Statements: Consolidated balance sheets at September 30, 2005 and 2004 14(a) For the years ended September 30, 2005, 2004 and 2003: Consolidated statements of income 13(a) Consolidated statements of cash flows 15(a) Consolidated statements of shareholders' equity 16(a) Notes to consolidated financial statements 16-23(a) Report of Independent Registered Certified Public Accounting Firm 24(a) Selected quarterly financial data (unaudited) 7(a) Consent of Independent Registered Certified Public Accounting Firm 22(b) Report of Independent Registered Certified Public Accounting Firm on Financial Statement Schedules 23(b) Consolidated Financial Statement Schedules: II - Valuation and qualifying accounts 24(b) III - Real estate and accumulated depreciation and Depletion 25-26(b) (a) Refers to the page number in the Company's 2005 Annual Report to Shareholders. Such information is incorporated by reference in Item 8 of this Form 10-K. (b) Refers to the page number in this Form 10-K. All other schedules have been omitted, as they are not required under the related instructions, are inapplicable, or because the information required is included in the consolidated financial statements. Exhibit 23(a) CONSENT OF INDEPENDENT REGISTERED CERTIFIED PUBLIC ACCOUNTING FIRM We hereby consent to the incorporation by reference in the Registration Statements on Form S-8 (Nos. 33-43215, 33-18878, 33- 55132 and 33-125099) of Patriot Transportation Holding, Inc. of our report dated December 22, 2005 relating to the financial statements, which appears in the Annual Report to Shareholders, which is incorporated in this Annual Report on Form 10-K. We also consent to the incorporation by reference of our report dated December 22, 2005, relating to the financial statement schedules, which appear in this Form 10-K. PricewaterhouseCoopers LLP Jacksonville, Florida December 27, 2005 ____________________ REPORT OF INDEPENDENT REGISTERED CERTIFIED PUBLIC ACCOUNTING FIRM ON FINANCIAL STATEMENT SCHEDULES To the Board of Directors of Patriot Transportation Holding, Inc.: Our audits of the consolidated financial statements referred to in our report dated December 22, 2005 appearing in the 2005 Annual Report to Shareholders of Patriot Transportation Holding, Inc. (which report and consolidated financial statements are incorporated by reference in this Annual Report on Form 10-K) also included an audit of the financial statement schedules listed in Item 15(a)(2) of this Form 10-K. In our opinion, these financial statement schedules present fairly, in all material respects, the information set forth therein when read in conjunction with the related consolidated financial statements. As described in Note 2, the consolidated financial statements for the years ended September 30, 2004 and 2003 have been restated. PricewaterhouseCoopers LLP Jacksonville, Florida December 22, 2005 ____________________ PATRIOT TRANSPORTATION HOLDING, INC. SCHEDULE II (CONSOLIDATED) - VALUATION AND QUALIFYING ACCOUNTS YEARS ENDED SEPTEMBER 30, 2005, 2004 AND 2003 ADDITIONS ADDITIONS BALANCE CHARGED TO CHARGED TO BALANCE AT BEGIN. COST AND OTHER AT END OF YEAR EXPENSES ACCOUNTS DEDUCTIONS OF YEAR Year Ended September 30, 2005: Allowance for doubtful accounts $ 638,320 $ 177,000 $ - $ 290,065(a) $ 525,255 Accrued risk insurance $6,653,657 $ 3,710,925 $ - $ 2,787,793(b) $7,576,789 Accrued health insurance 1,205,334 2,938,379 - 2,947,551(b) 1,196,162 Totals - insurance $7,858,991 $ 6,649,304 $ 0 $ 5,735,344 $8,772,951 Year Ended September 30, 2004: Allowance for doubtful accounts $ 565,744 $ 168,000 $ - $ 95,423(a) $ 638,320 Accrued risk insurance $6,779,345 $ 3,562,400 $ - $ 3,688,088(b) $6,653,657 Accrued health insurance 1,256,845 3,075,521 - 3,127,032(b) 1,205,334 Totals - insurance $8,036,190 $ 6,637,921 $ 0 $ 6,815,120 $7,858,991 Year Ended September 30, 2003: Allowance for Doubtful accounts $ 474,000 $ 157,537 $ - $ 65,793(a) $ 565,744 Accrued risk insurance $6,326,406 $ 4,151,065 $ - $ 3,698,126(b) $6,779,345 Accrued health Insurance 1,111,808 2,570,287 - 2,425,250(b) 1,256,845 Totals - insurance $7,438,214 $ 6,721,352 $ 0 $ 6,123,376 $8,036,190 (a) Accounts written off less recoveries (b) Payments <TABLE> PATRIOT TRANSPORTATION HOLDING, INC. SCHEDULE III (CONSOLIDATED)-REAL ESTATE & ACCUMULATED DEPRECIATION AND DEPLETION SEPTEMBER 30, 2005 (dollars in thousands) <CAPTION> Cost capi- Gross amount Year Deprecia- Encumb- Initial talized at which Accumulated Of Date tion Life County rances cost to subsequent carried at Depreciation Constr- Acquired Computed Company to acqui- end of period tion on: sition (a) <S> <C> <C> <C> <C> <C> <C> <C> Construction Aggregates Alachua, FL $ 1,442 $ 0 $ 1,442 $ 96 n/a 4/86 unit Clayton, GA 369 0 369 5 n/a 4/86 unit Fayette, GA 20 685 0 685 55 n/a 4/86 unit Hernando, FL 3,174 325 3,499 971 n/a 4/86 unit Lake, FL 1,485 0 1,485 1,086 n/a 4/86 unit Lee, FL 4,690 6 4,696 5 n/a 4/86 unit Levy, FL 1,281 104 1,385 502 n/a 4/86 unit Marion, FL 1,180 0 1,180 599 n/a 4/86 unit Monroe, GA 792 0 792 250 n/a 4/86 unit Muscogee, GA 369 0 369 148 n/a 4/86 unit Polk, FL 121 0 121 75 n/a 4/86 unit Prince Wil. VA 298 0 298 298 n/a 4/86 unit Putnam, FL 15,002 49 15,051 3,447 n/a 4/86 unit 20 30,888 484 31,372 7,537 Other Rental Property Wash D.C. 2,957 7,222 10,179 1,677 n/a 4/86 15 yr. Wash D.C. 3,811 0 3,811 0 n/a 10/97 Putnam, FL 326 50 376 341 n/a 4/86 5 yr. Spalding, GA 20 0 20 0 n/a 4/86 0 7,114 7,272 14,386 2,018 Commercial Property Baltimore, MD 0 439 3,338 3,777 1,635 1990 10/89 31.5 yr. Baltimore, MD 1,897 950 6,257 7,207 2,513 1994 12/91 31.5 yr. Baltimore, MD 2,383 690 2,837 3,527 555 2000 7/99 31.5 yr. Baltimore, MD 0 5,634 844 6,478 0 2001 8/95 31.5 yr. Duval, FL 0 2,416 529 2,945 2,526 n/a 4/86 25 yr. Harford, MD 2,501 31 3,826 3,857 943 1998 8/95 31.5 yr. Harford, MD 4,226 50 5,562 5,612 1,011 1999 8/95 31.5 yr. Harford, MD 5,858 85 6,665 6,750 1,246 2001 8/95 31.5 yr. Harford, MD 0 92 1,479 1,571 0 n/a 8/95 31.5 yr. Harford, MD 4,303 88 5,823 5,911 870 n/a 8/95 31.5 yr. Harford, MD 3,335 155 4,996 5,151 830 2001 8/95 31.5 yr. Howard, MD 3,766 2,859 3,734 6,593 2,263 1996 9/88 31.5 yr. Howard, MD 2,154 2,473 613 3,086 503 2000 3/00 31.5 yr. Anne Arun, MD 3,002 715 6,690 7,405 3,651 1989 9/88 31.5 yr. Anne Arun, MD 7,739 950 13,055 14,005 911 n/a 5/98 31.5 yr. Anne Arun, MD 9,716 1,525 10,658 12,183 56 2001 8/04 31.5 yr. Anne Arun, MD 0 1,307 198 1,505 0 n/a 1/03 31.5 yr. Norfolk, VA 0 7,512 0 7,512 222 1971 10/04 31.5 yr. Newcastle Co. DE 0 11,559 696 12,255 490 n/a 4/04 31.5 yr. 50,880 39,530 77,800 117,330 20,225 Investment Property 1,033 112 1,145 36 n/a 4/86 n/a GRAND TOTALS $50,900 $78,565 $85,668 $164,233 $29,816 </TABLE> (a) The aggregate cost for Federal income tax purposes is $147,392. PATRIOT TRANSPORTATION HOLDING, INC. SCHEDULE III (CONSOLIDATED) - REAL ESTATE AND ACCUMULATED DEPRECIATION AND DEPLETION YEARS ENDED SEPTEMBER 30, 2005, 2004 AND 2003 (In thousands) 2005 2004 2003 Gross Carrying Cost of Real Estate: Balance at beginning of period $146,995 145,803 133,925 Additions during period: Amounts capitalized 17,330 17,510 13,319 Deductions during period: Cost of real estate sold 92 16,318 1,441 Other (abandonments) - - - Balance at close of period $164,233 146,995 145,803 Accumulated Depreciation & Depletion: Balance at beginning of period $ 26,328 33,497 31,395 Additions during period: Charged to cost & expense 3,580 3,229 2,784 Deductions during period: Real estate sold 92 10,398 682 Balance at close of period $29,816 26,328 33,497