The search began after the 26-foot vessel was found unoccupied and adrift near the marina around 6:45 a.m., U.S. Coast Guard spokeswoman Lt. Heather Lampert said.
The missing boater associated with the vessel is a San Francisco sheriff's deputy who is on his day off, San Francisco sheriff's spokeswoman Susan Fahey said. The deputy has been identified as 56-year-old Michael Roberts.
Lampert said the boat had keys in the ignition and there was a cellphone onboard.
"It shows someone was recently aboard," she said.
Vallejo police Lt. Kenny Park said the deputy's wallet was also found on the fishing boat.
ABC7 News contributed to this report.