USS Alligator may refer to:
- USS Alligator (1809) was a schooner built in 1809 as Gunboat No. 166 and named Alligator in 1812
- USS Alligator (1813) was a sloop purchased in 1813. The British captured her on 14 December 1814 during the Battle of Lake Borgne.
- USS Alligator (1820) was a schooner, launched in 1820, and scuttled in 1822
- Alligator was a non-commissioned submarine launched in 1862 and sank in April 1863.
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