There are a few displays relevant to the Civil War in the museum

Antebellum structures in the downtown Pensacola Historic District

Old Christ Church completed in 1832 is one of the oldest surviving church buildings in Florida, serving the Pensacola community as an Episcopal Church, public library and museum. The building was also occupied by Federal troops during the Civil War.

The Old Chimney of the Hyer-Knowles Planing Mill- The chimney was part of the steam power plant for the Hyer-Knowles Mill. In March 1862, General Braxton Bragg was evacuating the Confederate forces holding Pensacola when Confederate Secretary of War Judah P. Benjamin gave the order to “Destroy all machinery private and public, which could be useful to the enemy; especially disable the sawmills in and around the Bay.” The machinery from the mills was loaded onto barges which were moved into Escambia Bay. On March 10th a thunderstorm and large waves sank the barges. That same night the Hyer-Knowles Mill was burned, and all that is left is the chimney.