The system, including some of the first railroads in Florida, stretched from Jacksonville west through Tallahassee and south to Tampa.

The two lines met at Lake City, Florida in 1860, and the latter also built from Tallahassee west to four miles (6 km) short of Quincy, Florida, stopping in 1863 in the middle of the American Civil War.

In 1872 it was reorganized again as the Atlantic, Gulf and West India Transit Company.

[7] The Seaboard Air Line Railway leased the FC&P on July 1, 1900, and the latter was merged into the former on August 15, 1903.

The FC&P tracks from Savannah, Georgia to Tampa, Florida via Jacksonville became part of Seaboard's main line.

By the time the Florida Central and Peninsular Railroad reached its greatest extent in 1893, it essentially had two main lines.

The other main line (the Southern Division) was what was previously the Florida Railroad extending from Fernandina Beach to Cedar Key.

Today, State Road 24 runs along much of the former right of way of the route between Waldo and Cedar Key.

[21] The Northern Division is now the following routes: The Leesburg and Indian River Railroad was incorporated in 1884 and merged into the Florida Railway and Navigation Company in 1885.

In 1891 the two companies merged into the East Florida and Atlantic Railroad, which was leased by the FC&P in 1892.

In the line's early days, passenger trains served the historic Church Street Station in Orlando, which belonged to the South Florida Railroad.

[25] The line west of Orlando remained intact under Seaboard and its successors until the 1970s when tracks were removed between Leesburg and Tavares.

[26] Since 1986, the remaining line from Tavares to Orlando has been operated by the Florida Central Railroad, a short line that was run by the Pinsly Railroad Company from 1986 to 2019 and is now operated by Regional Rail, LLC.

The Wannee Branch was originally part of the Atlantic, Suwannee River and Gulf Railway.

[28] The branch remains in service as part of CSX's Brooker Subdivision from Starke to a point just west of LaCrosse.

This created an alternate route into Tampa, which the Seaboard Air Line designated as the Brooksville Subdivision.

The Seaboard Air Line later leased this branch to the Ocala Northern Railroad in 1909.

The Ocala Northern was reorganized as the Ocklawaha Valley Railroad in 1915, but the line was abandoned by 1922.

The Florida Park Service currently maintains it as the Tallahassee-St. Marks Historic Railroad State Trail.