Apalachicola at the time of the Civil War was the third busiest port in the Gulf after Mobile and New Orleans. When the Civil War began there were no fortifications or vessels to protect the town. Military companies were raised but there were no weapons to arm them. Early in June two old 32-pounder cannon were forwarded to Apalachicola by Governor Milton. They were placed along the waterfront. As more cannon became available more extensive fortifications were built. These efforts were circumvented by Colonel Edward Hopkins of the 4th Florida Infantry. To protect the entrance to the bay he had a fort constructed on St. Vincent Island to guard West Pass. Hopkins then moved the cannons from Apalachicola to St. Vincent Island leaving the town defenseless. Governor John Milton was infuriated. He promised to garrison the town with state troops if Colonel Hopkins was removed. Hopkins was reassigned and Milton called up state troops to garrison Apalachicola.  The fort on St. Vincent Island was abandoned and all the cannon returned to the mainland, where eight gun batteries were erected to protect the town.  These batteries would never see action. In early 1862 the state legislature abolished the state troops, leaving Apalachicola without a garrison. The guns and their carriages were evacuated upriver in March 1862, leaving Apalachicola again defenseless. Most of the population left for the duration of the war.

On March 24th Commander H.W. Stellwagen of the USS Mercedita landed under a flag of truce. They found parts of a dozen white families still in the city, some Spanish fisherman, and women and children, a total of 500-600 people. They destroyed the sand batteries in the town and the battery on St. Vincent Island. Neither side garrisoned the town for the remainder of the war.