The second USS Bonita (SP-540) was a United States Navy patrol vessel commissioned in 1917 and sunk in 1918.

Bonita was built as a private pleasure craft by the Holmes Motor Company at Mystic, Connecticut.

On 17 May 1917, the U.S. Navy acquired her from her owner, Mr. Robert Windsor of Boston, Massachusetts, for use as a section patrol vessel during World War I.

Assigned to the 1st Naval District, Bonita operated on patrol duties in Boston Harbor for the rest of World War I.

Repeated efforts to locate Bonita's wreck proved unsuccessful, and she was stricken from the Navy List on 18 December 1918.