The fire broke out around 4:40 a.m. Sunday near 51 Port of Spain Road, by the Coronado Cays, south of Silver Strand State Beach, Bechtold said.
When fire crews from Coronado and Imperial Beach arrived, the flames were well involved.
Crews managed to contain the fire to the boat of origin.
Coast Guard officials spent Sunday morning fishing out parts of the boat that fell into the water.
No one was injured.
No further information was available.