USS Alligator, the fourth United States Navy ship of that name, is the first known U.S. Navy submarine, and was active during the American Civil War. During the Civil War the Confederate States Navy would also build its own submarine, H. L. Hunley.

H. L. Hunley, also known as the Hunley, CSS H. L. Hunley, or CSS Hunley, was a submarine of the Confederate States of America that played a small part in the American Civil War. Hunley demonstrated the advantages and dangers of undersea warfare. She was the first combat submarine to sink a warship (USS Housatonic), although Hunley was not completely submerged and, following her attack, was lost along with her crew before she could return to base. Twenty-one crewmen died in the three sinkings of Hunley during her short career. She was named for her inventor, Horace Lawson Hunley, shortly after she was taken into government service under the control of the Confederate States Army at Charleston, South Carolina.