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Flanagan quit after he was last month deregistered by the NRL for flouting his 2014 suspension for his part in the club’s peptides scandal.
With just five weeks until the club’s first trial against Manly at Lottoland, Sharks assistant John Morris has been appointed interim head coach, however, it’s not known whether he will permanently take over.
Flanagan said he would respond to the NRL’s show-cause notice but said he was standing down so that the club could get on with his job.
“This was obviously one of the toughest decisions of my 36-year rugby league career to resign from the head coaching role at Cronulla,” Flanagan said. “The last month has taken an enormous mental and emotional toll on my family and myself.
“I have made this decision in the best interests of the entire club and the players to allow the best possible preparation for the 2019 season without constant speculation and uncertainty as to who their head coach will be.
“I want to thank the Cronulla board and management, both past and present, as well as my dedicated coaching staff, all of whom I have worked closely with over seven seasons.”