Crews from the Greater Naples Fire Rescue District and Marco Island Fire-Rescue Department responded to the blaze at 12:13 p.m., said Nolan Sapp, assistant chief for Greater Naples.
"They've got it knocked down, but they're still doing fire attack," he said early Monday afternoon.
The fire appears to have sparked on the large yacht and spread from there to two smaller cabin cruisers, 28 feet long and 30 feet long, Sapp said.
"They were moored next to the big one," he said.
No one was hurt in the blaze, and the cause of the fire is not yet known. Greater Naples Fire officials are investigating the fire, Sapp said. Depending on their findings, the state fire marshal may investigate, he said.
Sapp said two of the three boats, including the large yacht, are a total loss. He estimated the total damage to be close to $1 million.
Using booms to create a barrier around the boats, a private contractor worked to keep fuel contained to the area, Sapp said.
"We don't want the fuel to contaminate the bay area," he said.