Charles Walker of Georgia and Kevin Bowling of Kentucky were found by a Florida Fish and Wildlife Conservation Commission officer.
A conservation commission plane and the Bay County sheriff's dive team were also looking for the men.
Someone on a boat near the empty anchored boat said he had seen no activity on the boat for nearly two hours.
SCUBA divers wear a vest that can be inflated either manually or with air remaining in a dive tank. They can stay afloat indefinitely.
The two men were found six miles south of Shell Island in the Florida Panhandle.
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