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Haynes, the opening batter who scored over 15,000 international runs for West Indies, was confirmed at a meeting of CWI's board of directors on Thursday.
He has signed a contract that runs until June 2024, and his role as selector will span two T20 World Cups and a 50-over World Cup.
Haynes has not been directly involved in the game in recent years, though was shortlisted as a candidate for West Indies men's head coach in 2019 before being beaten to the role by Phil Simmons.
"I would like to thank president [Ricky] Skerritt and the CWI board of directors for giving me the opportunity to serve West Indies cricket once again," Haynes said. "Being a selector is a thankless task, but a critical role in our cricket system and I am honoured to be appointed.
"I have always indicated that I would assist West Indies cricket in any way possible and I see this as an opportunity to do just that. I pledge to carry out my duties in a fair and professional manner."
Haynes takes over from Harper, whose two-year contract expired at the end of 2021. Jimmy Adams, CWI's director of cricket, was responsible for the appointment of a successor, with Simmons picking the squads for the upcoming white-ball series against Ireland and England.
Meanwhile, Ramnaresh Sarwan has been added to the selection panel for the men's senior and youth-level teams. He has stepped down from his role as chair of the Guyana Cricket Board to avoid any conflict of interest.