The vessel, a 40-foot Cuddy Cabin, caught fire about 1 p.m. in waters off the Westpoint Harbor marina, according to the U.S. Coast Guard.
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Two people abandoned the burning vessel and were picked up by a nearby boat. Information about whether anyone was injured was not immediately available.
The Redwood City Fire Department, San Francisco Airport Fire Boat and San Francisco Fireboat 1 responded to the blaze.