CSS Ellis (later USS Ellis) was a gunboat in the Confederate States Navy and the United States Navy during the American Civil War. It was lost during a raid while under command of famed Navy officer Lieutenant William B. Cushing.
The Ellis was purchased at Norfolk, Virginia in 1861 by the State of North Carolina and turned over to the Confederacy when that State became a member. With Commander W. T. Muse, CSN, in command, she played an important part in the defense of Fort Hatteras and Fort Clark in Hatteras Inlet, North Carolina on August 28–29, 1861, of Roanoke Island on February 7–8, 1862, and of Elizabeth City, North Carolina on February 10, 1862; that day she was captured by the Union Army after a desperate struggle in which her commander, Lieutenant James W. Cooke, CSN, was badly wounded.
Ellis was taken into the U.S. Navy and assigned to the North Atlantic Blockading Squadron. She was placed under the command of Lieutenant C. L. Franklin, USN, and spent her entire U.S. Navy service in the sounds and rivers of North Carolina.
Ellis took part in a combined expedition which captured Fort Macon, near Beaufort, North Carolina, on April 25, 1862. She had a brief engagement with Confederate cavalry off Winton, North Carolina on June 27, and from August 15 to 19 she made an expedition to Swansboro, North Carolina to destroy salt works and a battery. On October 14, she was detailed to the blockade of Bogue Inlet, and a week later, captured and burned the schooner Adelaide with a valuable cargo of turpentine, cotton, and tobacco.