The fire began early Sunday in the water behind Clipper Cove town homes on Okaloosa Island, according to the Okaloosa County Sheriff's Office.
Someone lives on the sailboat, but was not aboard at the time of the fire. The boat was not docked, but moored to a seawall near the town house complex.
There were no injuries, according to OCSO officials.
Firefighters from Fort Walton Beach Fire Department and Destin Fire Rescue assisted Okaloosa Island Firefighters. The Coast Guard, OCSO and Okaloosa EMS also responded to the scene.
The cause of the fire is not currently known. The State Fire Marshal's Office and Florida Fish and Wildlife are investigating.