USS Muscoota, was a 1370-ton Mohongo-class iron "double-ender" steam gunboat of the United States Navy during the American Civil War.

She was at Norfolk, Virginia, in May 1865 when ordered to Key West as part of an effort to prevent Confederate President Jefferson Davis escaping abroad.

Muscoota remained in the Gulf of Mexico area at least until August 1866, when she was sent north in response to a serious outbreak of yellow fever among her crew.

George Westinghouse, future inventor and businessman, served aboard the warship as an engineer.

The ship had only a short civilian career, as she was destroyed by fire near Little River, North Carolina, on 29 June 1870.