The fire began just before 6 a.m. on a boat at the end of the U Dock in Upper Santa Cruz Harbor.
The cause of the fire is unknown, and fire inspectors were at the scene late Tuesday morning.
A man who was thought to be on board one of the boats that burned, and who was briefly considered missing, was found to be at work.
Doug Schroedel, whose boat was moored next to the one where the fire started, said he woke up to at least two loud explosions just before 6 a.m. and saw an orange glow outside.
“The boat was engulfed in flames right next to me,” he said.
Schroedel said he quickly got dressed and was trying to leave his boat 15 seconds later.
Blocked from the dock by the intense heat, and hesitant to jump into the cold water, Schroedel clung to a piling as he cut away a dinghy with a knife, and then rowed to safety.
In addition to having his boat destroyed, Schroedel said he lost all his possessions in the fire.
Officials were planning to tow one of the damaged vessels to a boatyard to be extinguished, said Santa Cruz Fire Capt. Jason Hajduk.
Firefighters were limited in their access to the blaze to the narrow walkway of the dock under the darkness of the chilly night sky. A massive pillar of brown and black smoke rose above the blaze and wafted over the harbor, fully enveloping the Murray Street Bridge.
Dozens of onlookers stood by watching the boats burn.
“I heard two explosions and I looked out the porthole and screamed, ‘Oh my god, the dock is on fire,’” said one woman who did not want her name used.
Santa Cruz Fire teamed up with Santa Cruz Police in evacuating several surrounding docks. Central Fire Protection District also responded.