During the course of four centuries, eight flags have flown over this area, starting with the French in 1562, followed by the Spanish and British. In 1812, the Patriots' flag flew, followed in short order by General Sir Gregor MacGregor's personal flag, the Green Cross of Florida, and then, for a brief period, the flag of Mexico. The United States formally took possession of the island in 1821. At the outbreak of the Civil War, the Confederate flag was raised over Fernandina and Fort Clinch, but it was lowered in 1862, when the town was the target of a Union fleet.

Today, Fernandina Beach's harbor provides mooring for a large and prosperous shrimping fleet; two local pulp mills produce linerboard for paper containers and chemical cellulose. A 50-block restored Victorian historical district, including redeveloped Centre Street, is located downtown.