Waldo Point Harbormaster Ted Rose said the fire started at one of the approximately 1,300-square-foot boats and spread to a second houseboat nearby.
A third houseboat sustained smoke damage, Rose said.
A tenant living on a boat at a nearby dock reported seeing an explosion that blew out the windows of one of the boats, according to Rose.
The fire was under way before the explosion, Rose said.
The houseboats are about the size of a double garage and are heated with natural gas, Rose said.
Each boat was home to two adults and no one was aboard the houseboats at the time of the fire, he said.
The fire is out and firefighters are mopping up, Rose said.
The Southern Marin Fire Protection District responded to the fire at the harbor near U.S. Highway 101 and North Bridge Boulevard.