Shortly before the end of the war in 1865, a fellow Confederate cavalry officer, Col. George Wythe Baylor (1832–1916) (brother of Confederate Arizona Governor Colonel John R. Baylor), killed Wharton in Houston, Texas, over a simmering dispute on military matters. The incident began with an argument on the street outside of the Fannin Hotel, the headquarters of Maj. Gen. John B. Magruder. The two officers had quarreled in the past, but this time Wharton came into Magruder's quarters and, as Baylor later claimed, called Baylor a liar. Baylor shot the unarmed Wharton and killed him instantly.[2] Baylor was tried three times before he was finally acquitted after the war.[3]
Bailey, Anne, "John Austin Wharton", The Confederate General, Vol. 6, Davis, William C., and Julie Hoffman (eds.), National Historical Society, 1991, ISBN0-918678-68-4.