Defensive coordinator Stephen Tate was named interim head coach.
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Saint Augustine's University will begin an immediate national search for a replacement.
"I would like to commend Coach Bowser for his leadership in the athletic department and love for our student-athletes," SAU President Dr. Christine McPhail said. "I would like to ask the entire university community to join me in wishing Coach Bowser success in his future endeavors."
Dr. Lin Dawson will assume athletic director duties effective immediately until the end of the academic year. A national search for a full-time athletic director will take place at the end of the school year.
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"David Bowser is the type of person you want on your side when defending from a foxhole, climbing a steep mountain, patrolling the sidelines, or when it is 4th-and-1 with time running out. He has the passion and drive to get things done," Dawson said. "Starting near ground zero, he has built a solid football talent base that should pay dividends for the next football leader.
"Most notably, I am appreciative of his work to revive the Hall of Fame Ceremony, initiate an Athletics fundraising program, gain the Retool Your School Home Depot Award, and to energize the Lawrence Coleman Golf Tournament," Dawson added.
Bowser held the head coaching job since November 2019. He became the interim AD in July 2020 and was named full-time athletic director in August 2021.