The current Bay Line Railroad operates between Panama City, Florida, and Dothan, Alabama, including a branch from Grimes to Abbeville, Alabama, reached via CSX Transportation trackage rights north of Dothan. A line also connects Dothan eastward to Hilton, Georgia. The railroad interchanges with CSX Transportation in Dothan and with the new Florida Gulf & Atlantic regional at the former Louisville & Nashville crossing at Cottondale, Florida. Interchange is also made with G&W property Hilton & Albany Railroad at Hilton, Ga.

The company's main line between Panama City and Dothan was completed in 1908 by predecessor Atlanta & Saint Andrews Bay Railroad (ASAB), with a vision of freight and passenger service all the way to Atlanta. That goal was never achieved, but the shortline railroad did provide steady freight traffic from the Panama City ports and, for a time, connecting passenger service from regional railroads to the Gulf beaches.

By the 1970s, the shortline was known colloquially as The Bay Line. Stone Container Corporation purchased the Atlanta & Saint Andrews Bay in 1987. Then in 1994 Stone sold the assets of the railroad to Rail Management Corporation, which created the new Bay Line Railroad company to operate the line. Genesee & Wyoming shortline operator acquired all the assets of Rail Management in 2005, including the Bay Line. Today the line is 154 miles long and handles aggregates, chemicals, coal, food and feed products, forest products, ores and minerals, steel, and scrap. Shops and offices remain at Panama City, Florida.