The island’s lighthouse connection began in 1873 when the Lighthouse Service moved the district's depot from Mare Island to the southeast side of Yerba Buena Island. In 1875 construction was completed on the 25 foot tower with a fifth order Fresnel lens. In 1886 another fifth order lens was replaced the previous one. In 1933, a tunnel was bored through Yerba Buena Island to serve as a link between the east and west sections of the Bay Bridge. The light was automated by the United States Coast Guard in 1958. It is currently an active aid to navigation and not open to the public.
Yerba Beuna Island was formerly known as Goat Island for the goats that were pastured on the island in the gold rush days. The name was retired in 1931 when the Spanish name was restored.
Even though the station is in very close proximity to the Bay Bridge, the lighthouse remains operational. The keeper’s quarters are now the home of the Coast Guard District Commander.