During the Civil War, Floridians fought under several different patterns of Confederate flags. The "Stars and Bars" flag, now called the Confederate first national pattern, was selected (without a formal vote) by the Confederate government in March 1861. Because of its similarity to the U.S. flag, the Stars and Bars was sometimes confused with the Stars and Stripes in the smoke of battle. Later, a more distinctive banner was designed to replace the Stars and Bars on the battlefield.
On January 8, 1861, two days before Florida's secession, Confederate sympathizers (the Third Regiment of Florida Volunteers) take control of Fort Clinch, already abandoned by Federal workers who had been constructing the fort.
General Robert E. Lee visits Fort Clinch in November 1861 and again in January 1862, during a survey of coastal fortifications.