The Bay Line Railroad is one of 14 short rail lines being sold to Genessee & Wyoming Incorporated GWI.
The company announced Thursday it bought Earl Durden's Rail Management Corporation for $243 million.
The package includes the Apalachicola Northern Railroad in Gulf County, which Durden acquired three years ago.
GWI owns Jacksonville based Rail Link, which will operate the Bay Line and the Apalachicola & Northern line.
It will mark the end of local ownership of the Bay Line, which was established as the Atlanta and St. Andrew Bay Railroad in 1908.