By the time of the Civil War, Fernandina (the word Beach was added to the city's name in 1947) on Amelia Island was Florida's principal east coast port with a deep-water harbor and the eastern terminus of the Florida Railroad which ran across the state to Cedar Key.

In March 1862, a Union fleet of some 26 vessels under the command of Navy Flag Officer Samuel F. DuPont arrived at Fernandina from its base at Port Royal, South Carolina.

Confederate troops had been withdrawn in the face of this overwhelming Union force and both Fernandina and nearby Fort Clinch were captured without violence. Most of the community's residents also fled the island for Confederate held areas in the interior.

For the remainder of the war, Fernandina was a center of operations for the Union navy's South Atlantic Blockading Squadron, a rest center for Union troops, and a base for Union raiding expeditions into the adjacent areas of Florida and Georgia. Various Union regiments and detachments of troops were stationed on Amelia Island through the course of the war, and occupied abandoned homes and other buildings in Fernandina. Fernandina also became a haven for Unionist refugees and escaped slaves from Florida and Georgia.

Information Provided by the Florida Department of State.