General Cooper was a career United States Army staff officer, serving during the Second Seminole War and the Mexican-American War. Although little-known today, Cooper was also the highest-ranking Confederate general during the American Civil War.
In 1827, Cooper married Sarah Maria Mason, becoming the brother-in-law of future Confederate diplomat James M. Mason and later the father-in-law of Union General Frank Wheaton. Sarah’s sister, Ann Maria Mason, was the mother of Confederate cavalry general Fitzhugh Lee, a nephew of Robert E. Lee, while her brother John Mason, was a son-in-law of Gen. Alexander Macomb. Cooper served as aide-de-camp for Gen. Macomb from 1828 to 1836 and under his supervision authored A Concise System of Instructions and Regulations for the Militia and Volunteers of the United States.
At the beginning of the Civil War, Cooper’s loyalties were with the South. His wife’s family was from Virginia, and he had a close friendship with Jefferson Davis, who had also been U.S. Secretary of War. One of his last official acts as Adjutant General of the U.S. Army was to sign an order dismissing Brig. Gen. David E. Twiggs from the army. Twiggs had surrendered his command and supplies in Texas to the Confederacy (and was shortly thereafter made a Confederate major general.) This order was dated March 1, 1861, and Cooper resigned six days later. He traveled to Montgomery, Alabama, at the time the Confederacy’s capital, to join the Confederate States Army.
On reaching Montgomery, Cooper was immediately given a commission as a brigadier general on March 16, 1861. He served as both Adjutant General and Inspector General of the Confederate Army, a post he held until the end of the war. Cooper provided much-needed organization and knowledge to the fledgling Confederate War Department, drawing on his years performing such duties as Adjutant General of the U.S. Army.
On May 16, 1861, Cooper was promoted to full general in the Confederate Army. He was one of five men promoted to the grade at that time, and one of only seven during the war, but with the earliest date of rank. Thus, despite his relative obscurity today, he outranked such luminaries as Albert Sidney Johnston, Robert E. Lee, Joseph E. Johnston, and P.G.T. Beauregard. Cooper reported directly to Confederate President Jefferson Davis. At the war’s end in 1865, Cooper surrendered and was paroled on May 3 at Charlotte, North Carolina.