Point Bonita was a treacherous location. In 1853, the steamship Tennesse ran aground at a location now known as Tennesse Cove. In 1854, the Clipper Ship San Francisco struck the rocks in the fog and sank just east of Point Bonita. Mariners insisted that a lighthouse be built.

Finally on April 30, 1855, the second order fresnel lens was lit in Point Bonita's first lighthouse, a tower that stood 306 feet above the sea. By 1856, the first fog signal was installed at the point. It was a 24 pound cannon. Retired Sergeant Edward Maloney would fire the cannon as needed. During one very foggy spell, Maloney fired the gun every half hour for three days and three nights with only two hours of rest. The cannon was replaced first by a bell-boat anchored near the bar. Later it was replaced by 1,500 pound fog bell hanging from a frame building near the tower's base.

Like Point Loma, the location of the first Point Bonita lighthouse was often obscured by fog making it useless to boats passing below. During the 1870's the light and fog signal were reestablished further down the cliff to its present location. This required that a tunnel be dug through solid rock for a distance of 118 feet to get to the site for the tower. The fog signal building was built in 1872. The tunnel was dug in 1976 along with the new light. The original lantern and lens was used from the old tower. The old tower was capped and used as a day marker for mariners. The new lighthouse was lit on February 1, 1877.

April 18, 1906 at 5:12 a.m. San Francisco was hit with the first shockwaves of the earthquake that would be responsible for destroying most of the city. The keeper's quarters at Point Bonita was destroyed but the original tower survived only to be torn down in 1907. A landslide in 1941 destroyed the narrow foot bridge to the point. The Coast Guard rebuilt a bridge then a suspension bridge to the light in 1954.

The light was automated in 1981 and is still maintained by San Francisco's Coast Guard group.

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