The fire happened just before 6 a.m. at Riverside Marina on Bald Eagle Drive.
Marco Fire Rescue said crews from Marco Island, the Marco Island Police Department, Greater Naples, and the city of Naples were all called to assist.
Crews found flames coming from the boat's pilothouse shortly after arriving.
At one point, crews were forced to move several other boats nearby to keep the fire from spreading.
An investigation revealed that the fire had started from the lower cabin of the yacht.
The owner was not onboard at the time of the fire.