With the outbreak of the Civil War in 1861, Hawes resigned his position in the U.S. Army to accept a commission as a captain in the 2nd Kentucky Cavalry. On June 16, 1861, Hawes was promoted to the rank of major, and ten days later was promoted to colonel. He later resigned this position to be commissioned a major in the regular Confederate Army. On March 5, 1862, Hawes was promoted to brigadier general at the request of Albert Sidney Johnston. He became the cavalry commander of the Confederate Western Department.