Visitors reported at 5:42 a.m. that the boat, "Dancing Wolf," had washed ashore at the beach just north of Fulton Street, park spokesman George Durgerian said.
Park rangers and U.S. Park police responded and found a man in his late 30s who was aboard the ship and appeared to be intoxicated, Durgerian said.
Authorities determined the man, whose name is not yet being released, was wanted on unrelated warrants and took him into custody, Durgerian said.
Park officials learned that the boat had been reported stolen out of Vallejo at 2:30 a.m., he said.
The boat remained at the beach as of 8 a.m. Its owner has been notified and is trying to arrange for the recovery of the vessel, Durgerian said.