USS Muscoota, was a 1370-ton Mohongo-class iron "double-ender" steam gunboat of the United States Navy during the American Civil War. The ship was built at Greenpoint, New York, and commissioned in January 1865. 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.