CSS Ellis was purchased at Norfolk, Va., in 1861. by the State of North Carolina and turned over to the Confederacy when that State became a member. With Comdr. W. T. Muse, CSN, in command she played an important part in the defense of Forts Hatteras and Clark in Hatteras Inlet, N.C., 28-29 August 1861, of Roanoke Island, 7-8 February 1862 and of Elizabeth City, N.C., on 10 February 1862; that day she was captured by the Union Army after a desperate struggle in which her commander, Lt. J. M. Cook, CSN, was badly wounded.

Ellis was taken into the Navy and assigned to the North Atlantic Blockading Squadron. She served well until 25 November 1862 when she grounded above the mouth of New River, N.C. She was set afire to prevent recapture and demolished by the explosion of her own magazine. Lt. William B. Cushing, USN, was her last commander.