Hayes, who had been head coach for the last six seasons, told the university that he would resign immediately, RocketCityNow.com reported Tuesday.
The Bulldogs, which failed to qualify for the SWAC basketball tournament, finished the 2016-17 regular season 2-27 overall and 2016 in SWAC play.
Hayes was 54-121 at AAMU with his best season being a 14-16 campaign in 2013-14.
“We thank Coach Haynes for his service and commitment to Alabama A&M University,” Athletic Director Bryon Hicks said in a statement. “We wish him the best.”
A search for a replacement will begin immediately, according to the school’s website.