At the start of the Civil War in 1861 Cooke joined the
Virginia State Navy, and entered the service of the
Confederacy in the following June. Later that year he was placed in command of the small
gunboat CSS Ellis, and was captured with her after a hard fight near
Roanoke Island, North Carolina on February 10, 1862. Wounded in that action and soon paroled, he was promoted to
commander in June 1862. Commander Cooke's next assignment was to oversee the construction of the
ironclad ram
CSS Albemarle, under construction at "Edward's Ferry" near modern-day
Scotland Neck, North Carolina, from January 1863. After many difficulties,
Albemarle was successfully completed in April 1864, and Cooke became her commanding officer. On April 19 and May 5, he took her into action against Federal forces, sinking one gunboat and disabling or driving off others. That June he was promoted to the rank of
captain and was later placed in charge of Confederate naval forces on North Carolina's internal waters, holding that position until the end of the Civil War in 1865. ==Late life and death==