On January 10, 1861, Florida seceded from the United States and Confederates took control of the tower. Given the lack of a navy, Confederate leaders decided to extinguish the light, therefore denying its signal to Union warships. After several artillery battles between Confederate batteries and Union ships, Southern forces were forced to abandon nearby Fort Pickens and leave the coastal region to the Navy in May, 1862. Shortly thereafter, the Union navy operated the lighthouse.
From 1865 to the present, the lighthouse has seen many changes. It was repainted to be both black and white, was given modern lenses and electricity, and was automated in 1965. Still an active lighthouse, the Coast Guard Auxiliary Flotilla 17 operate both the lighthouse and museum.