USS R-16 (SS-93) was an R-class coastal and harbor defense submarine of the United States Navy.

R-16 departed Pearl Harbor on 12 December 1930 and, after transiting the Panama Canal, proceeded to Philadelphia, Pennsylvania, where she decommissioned on 12 May 1931.

Ordered back to the United States East Coast in the fall of 1941, she arrived at Key West, Florida, on 9 December 1941, two days after the Japanese attack on Pearl Harbor which brought the United States into World War II.

By 18 December 1941, she was at New London, Connecticut, from which she conducted patrols and assisted in antisubmarine warfare training into February 1942.

On 7 December 1942, the United States Army transport USAT Florida mistook R-16 for a German U-boat and opened gunfire on her in the Caribbean Sea, but R-16 submerged and avoided damage.