When the Civil War ended, the Union took control of Florida's government and

Florida joined the Confederate States of America at the beginning of the Civil War, as third of the original seven states to secede from the Union, following Lincoln's 1860 election. With the smallest population, nearly half of them slaves, Florida could only send 15,000 troops to the Confederate States Army. Its chief importance was in food-supply to the south, and support for blockade-runners, with its long coastline full of inlets, hard to patrol.

On the outbreak of war, the Confederates seized many of the state's army camps, though the Union retained control of the main seaports. There was little fighting in Florida, the only major conflict being the Battle of Olustee near Lake City in February 1864. However, wartime conditions made it easier for slaves to escape, and many of them became useful informers to Union commanders. As southern morale suffered, deserters from both sides took refuge in Florida, often attacking Confederate units and looting farms. Tallahassee became the second-last Confederate state capital to fall to the Union army. In May 1865, Federal control was re-established, slavery abolished, and the state governor John Milton shot himself, rather than submit to Union occupation.