The Yerba Buena Tunnel runs through its center and connects the western and eastern spans of the San Francisco–Oakland Bay Bridge, linking the city with Oakland, California.

the military reservation southeast of the Yerba Buena Tunnel belongs to the United States Coast Guard (USCG) District Eleven.

The US Coast Guard Sector San Francisco – Vessel Traffic Service (VTS) tower is located on Signal Road Building 278 atop the peak of the island.

During the summer of 2011, the Department of Homeland Security / United States Coast Guard opened the new SAFE Port Act (2006) Interagency Operations Center (IOC at Building 100 site on Spindrift Circle) on the US Coast Guard Sector / Station San Francisco base.

The IOC houses the VTS, WatchKeeper and the US Coast Guard Sector San Francisco Command Center together in one building.

The plant has a fragrance like spearmint, also commonly referred to as yerba buena, so the name was applied to Clinopodium douglasii as well.

On March 3, 1871, Representative Stephen L. Mayham of the Subcommittee on Private Land Claims reported an unsuccessful claim by Thomas H. Dowling that he had purchased Yerba Buena Island on September 10, 1849, from Gorham Hyronemo Nye, who had received the island in 1835 "as a compensation for transporting the body of the deceased Governor José Figueroa from Monterey to Santa Barbara".

The Torpedo Station was abandoned in the 1930s but still stands today (hidden underneath the San Francisco-Oakland Bay Bridge) listed in the National Register of Historic Places.

[8] Its Classic Revival style, fashionable for private residences in the Bay Area at the time, was unusual for naval base housing.

[9][10] His funeral was at the base chapel on Treasure Island and he was buried with full military honors at Golden Gate National Cemetery in San Bruno.

In 1996, the naval base and the Presidio of San Francisco were decommissioned and opened to public control under these types[clarification needed] of stipulations.

The San Francisco Police Department (SFPD) took over law enforcement jurisdiction of non-USCG parcels of Yerba Buena Island.

Beechey noted that the rock could be avoided by aligning the northern tip of Yerba Buena Island with two especially large redwood trees growing in the hills above Oakland as one entered the bay.

Hill Park near Treasure Island Road and Macalla Road used to be a military cemetery until the high visibility traffic approach to the 1939 Golden Gate International Exposition necessitated its removal and transfer of graves to the San Francisco National Cemetery in the Presidio of San Francisco.

[12] In 2011, the San Francisco Board of Supervisors approved a 20-year development of the island that aims to build two neighborhoods with up to 8,000 residences, of which 25 percent are designated for affordable housing.