| Name | Mark | System | From | To | Successor | Notes |
| Alabama and Florida Railroad (1853–1869) | | L&N | 1853 | 1869 | Pensacola and Louisville Railroad | - |
| Alabama and Florida Railroad (1898–1900) | | L&N | 1898 | 1900 | Louisville and Nashville Railroad | - |
| Alabama and Florida Railroad (1936–1941) | | | 1936 | 1941 | Ceased operations in 1941 | - |
| Alabama and Florida Railroad (1986–1992) | AFLR | | 1986 | 1992 | Alabama and Florida Railway | - |
| Alabama and Florida Railway | AF | | 1992 | 2011 | Ceased operations in 2011 | - |
| Alabama and Western Florida Railroad | | | 1926 | 1939 | | - |
| Alabama, Florida and Gulf Railroad | | | 1917 | 1936 | Alabama and Florida Railroad | - |
| Alabama, Florida and Southern Railroad | | | 1910 | 1917 | Alabama, Florida and Gulf Railroad | - |
| Alafia, Manatee, and Gulf Coast Railroad | | SAL | 1897 | 1906 | Charlotte Harbor and Northern Railway | - |
| Andalusia, Florida and Gulf Railway | | | 1919 | 1925 | N/A | |
| Apalachicola Northern Railroad | AN | | 1903 | | Later served by the AN Railway, the line is abandoned. | - |
| Arcadia, Gulf Coast and Lakeland Railroad | | | 1891 | 1893 | Florida, Peninsular and Gulf Railroad | - |
| Arlington and Atlantic Railway | | FEC | 1892 | 1892 | Jacksonville and Atlantic Railroad | - |
| Atlanta and St. Andrews Bay Railway | A&SA, ASAB | | 1906 | 1993 | Bay Line Railroad | - |
| Atlantic Coast Line Railroad | ACL | ACL | 1902 | 1967 | Seaboard Coast Line Railroad | - |
| Atlantic Coast, St. Johns and Indian River Railway | | FEC | 1883 | 1899 | Southeastern Railway | - |
| Atlantic and East Coast Terminal Company | | ACL/ FEC | 1905 | | | - |
| Atlantic and Gulf Railroad | A&G | ACL | 1866 | 1879 | Savannah, Florida and Western Railway | - |
| Atlantic, Gulf and West India Transit Company | | SAL | 1872 | 1881 | Florida Transit Railroad | - |
| Atlantic, Suwannee River and Gulf Railroad | | SAL | 1893 | 1893 | Atlantic, Suwannee River and Gulf Railway | - |
| Atlantic, Suwannee River and Gulf Railway | | SAL | 1893 | 1909 | Seaboard Air Line Railway | - |
| Atlantic, Valdosta and Western Railway | | SOU | 1897 | 1902 | Georgia Southern and Florida Railway, St. Johns River Terminal Company | - |
| Atlantic and Western Railroad | | FEC | 1888 | 1896 | Florida East Coast Railway | - |
| Augusta, Tallahassee and Gulf Railroad | | SAL | 1888 | 1891 | Carrabelle, Tallahassee and Georgia Railroad | - |
| Birmingham, Columbus and St. Andrews Railroad | | | 1903 | 1926 | Alabama and Western Florida Railroad | - |
| Blue Spring, Orange City and Atlantic Railroad | | FEC | 1878 | 1887 | Atlantic and Western Railroad | - |
| Bradford Farms Railroad | | | | | | Prison Spur between Raiford and Lawtey |
| Brooksville and Hudson Railroad | | | 1902 | 1907 | Tampa Northern Railroad | - |
| Brooksville and Inverness Railway | | SAL | 1925 | 1946 | Seaboard Air Line Railroad | - |
| Burlington Northern Inc. | BN | | 1980 | 1981 | Burlington Northern Railroad | - |
| Burlington Northern Railroad | BN | | 1981 | 1996 | Burlington Northern and Santa Fe Railway | - |
| Burlington Northern and Santa Fe Railway | BNSF | | 1996 | 1997 | Alabama and Gulf Coast Railway | - |
| Carrabelle, Tallahassee and Georgia Railroad | | SAL | 1891 | 1906 | Georgia, Florida and Alabama Railway | - |
| Central of Georgia Railway | CG | CG | 1904 | 1939 | N/A | - |
| Charlotte Harbor and Northern Railway | | SAL | 1906 | 1946 | Seaboard Air Line Railroad | - |
| Chattahoochee and East Pass Railway | | ACL | 1881 | 1884 | Savannah, Florida and Western Railway | - |
| DeLand and St. John's River Railroad | | ACL | 1886 | 1890 | Jacksonville, Tampa and Key West Railway | - |
| East Florida Railway | | ACL | 1880 | 1884 | Savannah, Florida and Western Railway | - |
| East Florida and Atlantic Railroad | | SAL | 1891 | 1893 | Florida Central and Peninsular Railroad | - |
| East and West Coast Railway | E&WC | SAL | 1913 | 1945 | Seaboard Air Line Railroad | - |
| Fellsmere Railroad | | | 1911 | 1924 | Trans-Florida Central Railroad | - |
| Fernandina and Amelia Beach Railway | | SAL | 1883 | 1894 | Florida Central and Peninsular Railroad | - |
| Fernandina and Jacksonville Railroad | | SAL | 1880 | 1884 | Florida Railway and Navigation Company | - |
| Florida Railroad | | SAL | 1853 | 1872 | Atlantic, Gulf and West India Transit Company | - |
| Florida Railway | | | 1905 | | | - |
| Florida Railway and Navigation Company | | SAL | 1884 | 1888 | Florida Central and Peninsular Railroad | - |
| Florida and Alabama Railroad | | | before 1914 | 1939 | N/A | |
| Florida, Alabama and Gulf Railroad | | | before 1911 | 1919 | Andalusia, Florida and Gulf Railway | |
| Florida, Atlantic and Gulf Central Railroad | | SAL | 1851 | 1868 | Florida Central Railroad | - |
| Florida Central Railroad | | ACL | 1907 | 1914 | Atlantic Coast Line Railroad | - |
| Florida Central Railroad | | SAL | 1868 | 1882 | Florida Central and Western Railroad | - |
| Florida Central and Gulf Railway | | SAL | 1916 | 1931 | N/A | - |
| Florida Central and Peninsular Railroad | | SAL | 1888 | 1903 | Seaboard Air Line Railway | - |
| Florida Central and Western Railroad | | SAL | 1882 | 1884 | Florida Railway and Navigation Company | - |
| Florida Coast and Gulf Railway | | FEC | 1892 | 1892 | Jacksonville, St. Augustine and Indian River Railway | - |
| Florida, Georgia and Western Railway | | SAL | 1891 | 1895 | Tallahassee Southeastern Railway | - |
| Florida Midland Railway | | ACL | 1883 | 1896 | Atlantic Coast Line Railroad | - |
| Florida, Peninsular and Gulf Railroad | | | 1893 | | | - |
| Florida Southern Railroad | | ACL | 1892 | 1903 | Atlantic Coast Line Railroad | - |
| Florida Southern Railway | | ACL | 1881 | 1892 | Florida Southern Railroad | - |
| Florida Steinhatchee Railway | | | | | | - |
| Florida Transit Railroad | | SAL | 1881 | 1883 | Florida Transit and Peninsular Railroad | - |
| Florida Transit and Peninsular Railroad | | SAL | 1883 | 1884 | Florida Railway and Navigation Company | - |
| Florida West Shore Railway | | SAL | 1903 | 1909 | Seaboard Air Line Railway | - |
| Florida Western Railroad | | SAL | 1881 | 1882 | Pensacola and Atlantic Railroad | - |
| Florida Western and Northern Railroad | | SAL | 1924 | 1945 | Seaboard Air Line Railroad | - |
| Fort Myers Southern Railroad | FMS | ACL | 1917 | 1987 | Atlantic Coast Line Railroad | - |
| Fort White and Southern Railway | | | 1896 | | | - |
| Fort Wilderness Railroad | FWRR | | 1974 | 1980 | | - |
| Gainesville and Gulf Railway | | SAL | 1895 | 1907 | Tampa and Jacksonville Railway | - |
| Gainesville, Ocala and Charlotte Harbor Railroad | | ACL | 1876 | 1881 | Florida Southern Railway | - |
| Gainesville, Rocky Point and Micanopy Railway | | SAL | 1884 | 1895 | Gainesville and Gulf Railway | - |
| Georgia and Florida RailNet | GFRR | | 1999 | 2005 | Georgia and Florida Railway | - |
| Georgia and Florida Railroad | GFRR | | 1995 | 1999 | Georgia and Florida RailNet | - |
| Georgia and Florida Railroad | G&F | G&F | 1926 | 1951 | Valdosta Southern Railroad | - |
| Georgia and Florida Railway | G&F | G&F | 1906 | 1926 | Georgia and Florida Railroad | - |
| Georgia, Florida and Alabama Railroad | GF&A | SAL | 1927 | 1974 | Seaboard Coast Line Railroad | - |
| Georgia, Florida and Alabama Railway | GF&A | SAL | 1901 | 1928 | Georgia, Florida and Alabama Railroad | - |
| Georgia Pine Railway | | SAL | 1895 | 1901 | Georgia, Florida and Alabama Railway | former logging railroad |
| Georgia Southern and Florida Railroad | | SOU | 1889 | 1895 | Georgia Southern and Florida Railway | - |
| Green Cove and Midland Railway | | | 1885 | 1892 | Southwestern Railroad | - |
| Green Cove Springs and Melrose Railroad | | | 1881 | 1885 | Green Cove and Midland Railway | - |
| Gulf Coast Railway | | | 1915 | 1921 | N/A | - |
Gulf, Florida and Alabama Railway
| DWR | SLSF | 1911 | 1922 | Muscle Shoals, Birmingham and Pensacola Railway | - |
| Gulf Ports Terminal Railway | | SLSF | 1916 | 1927 | Muscle Shoals, Birmingham and Pensacola Railroad | - |
| Halifax and Indian River Railway | | FEC | 1891 | 1892 | Florida Coast and Gulf Railway | - |
| Inland Lakes Railway | | | 2005 | 2009 | | Former tourist railroad in Tavares. |
| Jacksonville and Atlantic Railroad | | FEC | 1892 | 1892 | Jacksonville and Atlantic Railway | - |
| Jacksonville and Atlantic Railway | | FEC | 1893 | 1900 | Florida East Coast Railway | - |
| Jacksonville Belt Railroad | | SAL | 1886 | 1888 | Florida Central and Peninsular Railroad | - |
| Jacksonville Bridge Company | | FEC | 1888 | 1892 | Florida Coast and Gulf Railway | - |
| Jacksonville, Gainesville, and Gulf Railway | | SAL | 1926 | 1943 | N/A | - |
| Jacksonville, Pensacola and Mobile Railroad | | SAL | 1869 | 1882 | Florida Central and Western Railroad | - |
| Jacksonville, St. Augustine and Halifax River Railway | | FEC | 1881 | 1892 | Florida Coast and Gulf Railway | - |
| Jacksonville, St. Augustine and Indian River Railway | | FEC | 1892 | 1895 | Florida East Coast Railway | - |
| Jacksonville and St. John's River Railway | | ACL | 1899 | 1899 | Savannah, Florida and Western Railway | - |
| Jacksonville and Southwestern Railroad | | ACL | 1899 | 1904 | Atlantic Coast Line Railroad | - |
| Jacksonville, Tampa and Key West Railway | | ACL | 1881 | 1899 | Atlantic Coast Line Railroad, Jacksonville and St. John's River Railway | - |
| Jacksonville Terminal Company | JTCO | ACL/ FEC/ SAL/ SOU | 1894 | 1978 | N/A | - |
| Jaxport Terminal Railway | JXPT | | 1989 | 1996 | Talleyrand Terminal Railroad | - |
| Jupiter and Lake Worth Railway | | | 1888 | 1895 | N/A | - |
| Kissimmee River Railway | | SAL | 1917 | | N/A | - |
| Lake Monroe and Orlando Railroad | | ACL | 1875 | 1879 | South Florida Railroad | - |
| Lake Wimico and St. Joseph Canal and Railroad Company | | | 1836 | 1841 | N/A | - |
| Leesburg and Indian River Railroad | | SAL | 1881 | 1884 | Florida Railway and Navigation Company | - |
| Live Oak and Gulf Railway | | | 1894 | 1904 | Suwannee and San Pedro Railroad | - |
| Live Oak and Perry Railroad | | SOU | 1903 | 1905 | Live Oak, Perry and Gulf Railroad | - |
| Live Oak, Perry and Georgia Railroad | | | 1995 | 1999 | Georgia and Florida RailNet | - |
| Live Oak, Perry and Gulf Railroad | | SOU | 1905 | 1971 | Live Oak, Perry and South Georgia Railway | - |
| Live Oak, Perry and South Georgia Railway | LPSG | SOU | 1971 | 1993 | Georgia Southern and Florida Railway | - |
| Live Oak and Rowland's Bluff Railroad | | ACL | 1881 | 1884 | Savannah, Florida and Western Railway | - |
| Live Oak, Tampa and Charlotte Harbor Railroad | | ACL | 1881 | 1884 | Savannah, Florida and Western Railway | - |
| Louisville and Nashville Railroad | L&N, LN | L&N | 1880 | 1983 | Seaboard System Railroad | - |
| Macon and Florida Air Line Railroad | | SOU | 1884 | 1889 | Georgia Southern and Florida Railroad | - |
| Madison Southern Railway | | | | 1922 | N/A | - |
| Marianna and Blountstown Railroad | M&BT, MBT | | 1909 | 1972 | N/A | - |
| Muscle Shoals, Birmingham and Pensacola Railroad | MSBP | SLSF | 1924 | 1928 | St. Louis – San Francisco Railway | - |
| Muscle Shoals, Birmingham and Pensacola Railway | MSBP | SLSF | 1922 | 1924 | Muscle Shoals, Birmingham and Pensacola Railroad | - |
| Naples, Seaboard, and Gulf Railway | | SAL | 1926 | | Seaboard Air Line Railroad | - |
| Ocala Northern Railroad | | | 1909 | 1915 | Ocklawaha Valley Railroad | - |
| Ocala and Southwestern Railroad | | | | 1923 | N/A | - |
| Ocklawaha Valley Railroad | | | 1915 | 1922 | N/A | - |
| Okeechobee Railroad | | | | | N/A | - |
| Orange Belt Railway | | ACL | 1885 | 1893 | Sanford and St. Petersburg Railroad | - |
| Orange Ridge, DeLand and Atlantic Railroad | | ACL | 1880 | 1886 | DeLand and St. John's River Railroad | - |
| Orlando and Winter Park Railway | | SAL | 1886 | 1891 | East Florida and Atlantic Railroad | - |
| Ormond Bridge Company | | FEC | 1887 | 1898 | Florida East Coast Railway | - |
| Osceola and Lake Jesup Railway | | SAL | 1889 | 1891 | East Florida and Atlantic Railroad | - |
| Palatka Bridge Company | | FEC | 1888 | 1893 | Jacksonville, St. Augustine and Indian River Railway | - |
| Palatka and Indian River Railway | | ACL | 1881 | 1887 | Jacksonville, Tampa and Key West Railway | - |
| Patterson and McInnis Sawmill Railway | P&M | | | 1940 | Georgia-Pacific | Former logging railroad |
| Pelham and Havana Railroad | | | 1906 | 1923 | N/A | - |
| Peninsular Railroad | | SAL | 1878 | 1883 | Florida Transit and Peninsular Railroad | - |
| Pensacola Railroad | | L&N | 1877 | 1880 | Louisville and Nashville Railroad | - |
| Pensacola, Alabama and Tennessee Railroad | | SLSF | 1892 | 1915 | Pensacola, Mobile and New Orleans Railway | - |
| Pensacola and Atlantic Railroad | | L&N | 1881 | 1891 | Louisville and Nashville Railroad | - |
| Pensacola and Fort Barrancas Railroad | | L&N | 1870 | 1882 | Florida Western Railroad | - |
| Pensacola Electric Company | | | 1906 | | | - |
| Pensacola Electric Terminal Railway | | | 1897 | 1906 | Pensacola Electric Company | - |
| Pensacola and Georgia Railroad | | SAL | 1853 | 1869 | Atlantic and Gulf Railroad, Tallahassee Railroad | - |
| Pensacola and Louisville Railroad | | L&N | 1868 | 1878 | Pensacola Railroad | - |
| Pensacola and Mobile Railroad and Manufacturing Company | | L&N | 1861 | 1881 | Louisville and Nashville Railroad | - |
| Pensacola, Mobile and New Orleans Railway | | SLSF | 1907 | 1917 | Gulf Ports Terminal Railway | - |
| Pensacola and Perdido Railroad | | SLSF | 1869 | 1915 | Pensacola, Mobile and New Orleans Railway | - |
| Pensacola Street Car Company | | | 1882 | 1891 | Pensacola Terminal Company | - |
| Pensacola Terminal Company | | | 1891 | 1897 | Pensacola Electric Terminal Railway | - |
| Plant System | | ACL | 1894 | 1902 | Atlantic Coast Line Railroad | - |
| Plant City, Arcadia, and Gulf Railroad | | SAL | 1905 | 1909 | Seaboard Air Line Railway | former logging railroad |
| Port Inglis Terminal Company | | SAL | | 1916 | Florida Central and Gulf Railway | - |
| Port St. Joe Dock and Terminal Railway | | | 1912 | 1929 | N/A | - |
| St. Andrews Bay Railway and Terminal Company | | | 1914 | | | - |
| St. Augustine and Halifax River Railway | | FEC | 1889 | 1893 | Jacksonville, St. Augustine and Indian River Railway | - |
| St. Augustine and Palatka Railway | | FEC | 1886 | 1889 | St. Augustine and Halifax River Railway | - |
| St. Augustine and South Beach Railway | | | 1886 | | | - |
| St. Cloud and Sugar Belt Railway | | ACL | 1888 | 1893 | South Florida Railroad | - |
| St. Johns Railway | | FEC | 1858 | 1893 | Jacksonville, St. Augustine and Indian River Railway | - |
| St. Johns and Halifax Railway | | FEC | 1881 | 1888 | St. Johns and Halifax River Railway | - |
| St. Johns and Halifax River Railway | | FEC | 1888 | 1893 | Jacksonville, St. Augustine and Indian River Railway | - |
| St. John's and Lake Eustis Railroad | | ACL | 1896 | 1902 | Atlantic Coast Line Railroad | - |
| St. John's and Lake Eustis Railway | | ACL | 1879 | 1896 | St. John's and Lake Eustis Railroad | - |
| St. Johns River Terminal Company | SJRT | SOU | 1901 | | | - |
| St. Louis – San Francisco Railway | SLSF | SLSF | 1928 | 1980 | Burlington Northern Inc. | - |
| Sanford and Everglades Railroad | | ACL | 1908 | 1913 | Atlantic Coast Line Railroad | - |
| Sanford and Indian River Railroad | | ACL | 1881 | 1893 | South Florida Railroad | - |
| Sanford and Lake Eustis Railroad | | ACL | 1885 | 1890 | Jacksonville, Tampa and Key West Railway | - |
| Sanford and St. Petersburg Railroad | | ACL | 1893 | 1903 | Atlantic Coast Line Railroad | - |
| Savannah, Florida and Western Railway | | ACL | 1876 | 1902 | Atlantic Coast Line Railroad | - |
| Seaboard Air Line Railroad | SAL | SAL | 1946 | 1967 | Seaboard Coast Line Railroad | - |
| Seaboard Air Line Railway | | SAL | 1900 | 1945 | Seaboard Air Line Railroad | - |
| Seaboard-All Florida Railway | | SAL | 1925 | 1945 | Seaboard Air Line Railroad | - |
| Seaboard Coast Line Railroad | SCL | | 1967 | 1983 | Seaboard System Railroad | - |
| Seaboard System Railroad | SBD | | 1983 | 1986 | CSX Transportation | - |
| Silver Springs, Ocala and Gulf Railroad | | ACL | 1875 | 1901 | Savannah, Florida and Western Railway | - |
| Silver Springs and Western Railroad | SS&W | SAL | 1895 | 1909 | acquired by Ocala Northern Railroad | |
| South Central Florida Railroad | SCFE | | 1990 | 1994 | South Central Florida Express, Inc. | - |
| South Florida Railroad | | ACL | 1879 | 1893 | Savannah, Florida and Western Railway | - |
| South Florida and Gulf Railroad | | | 1914 | 1918 | N/A | - |
| South Georgia Railway | | SOU | 1900 | 1971 | Live Oak, Perry and South Georgia Railway | - |
| Southeastern Railway | | FEC | 1899 | 1902 | Florida East Coast Railway | - |
| Southwestern Railroad | | | 1892 | 1899 | N/A | - |
| Standard and Hernando Railroad | | SAL | 1903 | 1916 | Florida Central and Gulf Railway | - |
| Starke and Sampson City Railroad | | SAL | 1890 | | Atlantic, Suwannee River and Gulf Railway | - |
| Suwannee and San Pedro Railroad | | | 1900 | 1905 | Florida Railway | - |
| Tallahassee Railroad | | SAL | 1834 | 1870 | Jacksonville, Pensacola and Mobile Railroad | - |
| Tallahassee, Perry and Southeastern Railway | | SAL | 1905 | 1909 | Seaboard Air Line Railway | - |
| Tallahassee Southeastern Railway | | SAL | 1895 | 1906 | Tallahassee, Perry and Southeastern Railway | - |
| Tampa and Gulf Coast Railroad | | SAL | 1913 | 1976 | Seaboard Coast Line Railroad | - |
| Tampa and Gulf Coast Railway | | SAL | 1909 | 1913 | Tampa and Gulf Coast Railroad | - |
| Tampa and Jacksonville Railway | | SAL | 1906 | 1927 | Jacksonville, Gainesville and Gulf Railway | - |
| Tampa Northern Railroad | TN | SAL | 1906 | 1946 | Seaboard Air Line Railroad | - |
| Tampa, Peace Creek and St. John's River Railroad | | ACL | 1878 | 1881 | Jacksonville, Tampa and Key West Railway | - |
| Tampa Southern Railroad | TAS | ACL | 1917 | 1982 | Atlantic Coast Line Railroad | - |
| Tampa Terminal Company | | SAL | 1906 | | | - |
| Tampa and Thonotosassa Railroad | | ACL | 1893 | 1901 | Savannah, Florida and Western Railway | - |
| Tampa Union Station Company | | ACL/ SAL | 1910 | 1968 | N/A | - |
| Tavares, Apopka and Gulf Railroad | | SAL | 1881 | 1890 | Tavares and Gulf Railroad | - |
| Tavares and Gulf Railroad | TV&G | SAL | 1890 | 1969 | Seaboard Coast Line Railroad | - |
| Tavares, Eustis & Gulf Railroad | TE&G | | 2011 | 2017 | | - |
| Tavares, Orlando and Atlantic Railroad | | SAL | 1881 | 1891 | Florida Central and Peninsular Railroad | - |
| Thomasville, Tallahassee and Gulf Railroad | | SAL | 1882 | 1888 | Augusta, Tallahassee and Gulf Railroad | - |
| Trans-Florida Central Railroad | | | 1924 | 1953 | N/A | - |
| Tropical Florida Railroad | | SAL | 1881 | 1883 | Florida Transit and Peninsular Railroad | - |
| United States and West Indies Railroad and Steamship Company | | SAL | 1900 | 1903 | Florida West Shore Railway | - |
| Valdosta Southern Railroad | VSO | | 1951 | 1972 | N/A | - |
| Valdosta Southern Railway | | G&F | 1895 | 1907 | Georgia and Florida Railway | - |
| Watertown and Northern Railway | | | | | | - |
| West Coast Railway | | SOU | 1900 | 1924 | South Georgia Railway | - |
| West India Fruit and Steamship Company | WIF | | 1946 | 1961 | N/A | - |
| Western Railway of Florida | | | 1886 | 1892 | Southwestern Railroad | Leased the Green Cove and Midland Railway |
| Winston and Bone Valley Railroad | | ACL | 1892 | 1909 | Atlantic Coast Line Railroad | - |
| Withlacoochee Railway | | G&F | 1893 | 1895 | Valdosta Southern Railway | - |
| Yalaha and Western Railroad | | ACL | 1900 | 1902 | Atlantic Coast Line Railroad | - |
| Yellow River Railroad | | SAL | 1887 | 1906 | Louisville and Nashville Railroad | - |