Ellis was launched in 1860, and purchased by the Confederate States Navy for use as a gunboat. Commissioned in 1861, CSS Ellis formed part of the Mosquito Fleet in North Carolina. Displacing just 100 tons, Ellis drew only 6 feet of water, making her well suited to riverine work. She was given a 32-pounder rifle and a 12-pounder howitzer, and had a crew of twenty-eight. Ellis was involved in the defense of Fort Clark in August, 1861, then in the Battle for Roanoke Island on 7-8 February, 1862. Two days later, Ellis was captured during the Battle of Elizabeth City. Recommissioned as USS Ellis, she was assigned to the blockade of the South, and remained in North Carolina. Ellis helped capture Fort Macon in April, fought with Confederate cavalry in June, and raided Swansboro in August. On 21 October, Ellis captured and burned the blockade runner Adelaide. While returning from a raid of Jacksonville, Ellis ran aground on 24 November, 1862. She was burned the next morning, to prevent recapture.