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Dakich, who nearly left Bowling Green five years ago to coach West Virginia, sent a letter to athletic director Greg Christopher, saying he would not seek an extension of his contract, which expires in June.
"Being involved with BGSU basketball has been a wonderful part of my life," Dakich wrote.
The Falcons finished this season with a 13-18 record.
Following a late-season overtime loss at Buffalo, Dakich made profanity-laced comments and said his team was cheated when officials called a technical foul for delay of game after he and his players left the court before the game was over.
Mid-American Conference Commissioner Rick Chryst called Dakich's comments unprofessional.
During his first five years, the Falcons made two NIT appearances and won the MAC regular-season title in 2002. The team's 24 victories that season were the school's most in more than a half century. Since then, Bowling Green has had losing seasons in four of the last five years.
Dakich in 2002 accepted the coaching job at West Virginia but abruptly walked away after a week. He didn't say why he changed his mind.
Dakich played and coached under Bob Knight at Indiana for 16
seasons before coming to Bowling Green.