The accident happened near the Clyde B Wells bridge off Highway 331. The accident was called in around 7:00am Monday morning after a passerby saw an 18-year-old boy in the water.
18-year-old Tyler Carpenter from Fort Walton Beach and his uncle, 41-year-old Robert Gregory went out around midnight to go floundering.
The boat was capsized sometime during the night.
Officials say, Carpenter had on his life-jacket and was able to make it back to shore.
He was taken to Sacred Heart Medical Center and was release around eleven.
Florida Wildlife has taken over case and the WCSO is still assisting.
FWC has four boats on scene, WCSO has two boats and has used the helicopter.
Teams have recovered the 6-horse power motor boat but are still searching the area for the uncle.