On January 10, 1861, Florida seceded from the United States. Union forces abandoned Fort Barrancas in favor of Fort Pickens, on the western end of Santa Rosa Island. The Confederates took control of the tower, and eventually discontinued the light and removed the lens. The opposing forces warily watched one another across the bay for months. Then on November 22, 1861, a two-day artillery battle erupted. The “Lighthouse Batteries” were frequent targets for the guns of Fort Pickens, and roughly half a dozen rounds struck the tower. Confederates evacuated the area on May 9, 1862, and the lighthouse fell under Union control. None of the rounds penetrated the outer wall of the lighthouse, and the tower was found to be in good condition. A fourth-order lens was placed in the lantern room, and the tower was lit again on December 20, 1862.
The original first-order Fresnel lens was recovered after the war, and was re-installed in the tower’s lantern room in 1869. That same year, a new dwelling was built for the keepers, and the tower’s day mark was changed. The bottom third of the tower remained white to stand out against the trees, but the top portion was painted black to stand out against a possibly cloud-filled sky.