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The former Wellington representative has previously coached the Fijian men's, women's and under-19 teams and worked as a batting consultant for the Bangladesh test side.
He also mentored the Wellington under-19 men's and women's teams plus the women's A side.
Morgan will start his new role on September 1.
"I’m really excited to move south and get stuck into it,’’ he said.
"The Magicians are a side with huge potential and I’m looking forward to playing my part and seeing how well they can do.
"My goal is to make a positive difference on everyone’s game, and if I can do that, then I’m sure we’ll see some good results along the way.”
“Rhys’ coaching experience and the qualities he brings to the table with regards to his coaching skill set is going to be valuable for this side,” he said.
“Rhys understands what it takes to coach at different development levels, across both male and female environments.
“His experience in the women’s game, as well as his proven ability to create learning environments that progress individual talent and promote team success is an exciting prospect for the Magicians,” Croy said.