The 50-year-old diver's daughter called California State Parks, which notified the Sonoma County Sheriff's Office, Deputy Debbie Little said.
A sheriff's helicopter responded shortly after 8 a.m. and searched the area for 45 minutes, Little said. The diver was not found, and poor visibility hampered the search, she said.
The diver was wearing a black wetsuit and a weight belt but no fins, Little said. He was last seen in the reef area before he went underwater.
Little said State Parks rangers and a sheriff's deputy assigned to the Sonoma Coast were still at the scene this morning.