Gene grew up in Erlanger, KY, and graduated from Centre College in Danville, KY, before joining the U.S. Air Force and attending Officer Training School (OTS) in the fall of 1987. He earned his master‘s degree at Florida State University while serving in the Air Force at Tyndall AFB, FL. 

As Brigadier General, Gene was the Air National Guard Assistant to the Commander, Air Force Global Strike Command, Barksdale Air Force Base, LA. The command organizes, trains, equips and maintains combat–ready forces that provide strategic deterrence, global strike and combat support to USSTRATCOM and other geographic combatant commands. The command is comprised of more than 33,700 professionals operating at two Numbered Air Forces and 11 active–duty, ANG and Air Force Reserve wings. Weapons systems assigned to the command include Minuteman III Intercontinental Ballistic Missiles, B–1, B–2 and B–52 bombers, UH–1 N helicopters, the E–4B National Airborne Operations Center aircraft and the Nuclear Command, Control and Communications systems. 

General Hughes previously served as Special Assistant to the Director, Air National Guard for Headquarters Air Force, Deputy Chief of Staff for Strategic Deterrence and Nuclear Integration (HAF/A10). General Hughes earned his commission in 1987 through the United States Air Force Officer Training School, Lackland Air Force Base, Medina Annex, Texas. He has served in various operational and staff assignments to include Senior Executive to the Director of the Air National Guard, and Chief, Joint Resources and Readiness Division (74) at North American Aerospace Defense Command (NORAD) and United States Northern Command (USNORTHCOM) as well as two group level commands. General Hughes has deployed in support of Operation Deliberate Force, Operation Deny Flight, Operation Iraqi Freedom, and Operation Enduring Freedom.

In July 2021, Gene was promoted to Major General. He retired from his career in both active-duty Air Force and full-time Air National Guard. He served part time in the Air National Guard as the Military Assistant to the Commander of US Air Force Global Strike Command until February 2023.