The incident happened in the Bay, in between the Golden Gate Bridge and Alcatraz Island. Video showed the boat fully sinking underwater.
Fire officials confirmed 16 other people have been rescued from the water. Nineteen total people were on board the boat.
An ABC7 Eyewitness News photographer on scene confirms at least one person was killed.
One dog aboard the vessel also died.
The fire department says that they received a call after 3:30 p.m. PT for a boat on fire. It was a pontoon-type boat.
San Francisco Mayor Daniel Lurie called the ongoing operation an "all-hands-on-deck" search and rescue mission.
Officials say 11 vessels are currently searching for the two missing. They say white caps on the water is challenging conditions
First responders took the boat passengers to the Fort Mason area in San Francisco.