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 During the war
On January 10, Florida became the third state to secede from the Union. On January 12, state troops seized the Navy Yard and Forts Barrancas and McRee. (Fort Pickens would remain under Union control for the duration of the war.)
On October 8, Confederate forces launched an unsuccessful offensive to capture Fort Pickens. Bragg's "Army of Pensacola" was organized on October 22. They would trade artillery exchanges with the Union-held Pickens several times in late 1861 and early 1862.
By March 1862, most of the Army of Pensacola's troops were absorbed into the Army of the Mississippi or transferred elsewhere. The last Confederate forces left on May 9, and Mayor John Brosnaham surrendered Pensacola to Union troops on May 10.
 Confederate veterans
A number of Confederate soldiers and leaders returned to Pensacola after the war, including a number of prominent citizens:
- Stephen Russell Mallory, Confederate Secretary of the Navy
- Augustus Emmet Maxwell, Confederate Senator
- Jackson Morton, Confederate Representative
- Edward Aylesworth Perry, Confederate Brigadier General and postwar Florida Governor
- Chandler Cox Yonge
- Nathan Burrell Cook
- William Franklin Lee
- Daniel Gonzalez Brent
- Henry Baars
- Robert Bell Smith Hargis
- John Ely Spoon, Pensacola's last surviving Confederate veteran
 Confederate memorial
Confederate sympathies remained strong in Pensacola following the war. Beginning in 1881, Pensacolian Edward Aylesworth Perry led a campaign to erect a state Confederate memorial in Tallahassee and began seeking donations. After his death, William Dudley Chipley moved the location of the memorial to Pensacola, where most of the donations had originated. It was built in Lee Square atop Gage Hill, opening in 1891, and was for many decades thereafter the site of annual Decoration Day celebrations.