Alleyne, 54, takes over T20 duties from Matthew Maynard, who has retained the red-ball role following Glamorgan's strong showing in last year's County Championship, while he will also oversee their 50-over fortunes, with David Harrison departing after guiding the club to the Royal London Cup in 2021.
The appointment marks a return to county coaching for Alleyne, who became the first Black British coach in English domestic history in 2004 when he took over the reins at Gloucestershire for three years, initially in a player-coach capacity.
Alleyne played a total of ten ODIs for England between 1999 and 2000, but he made his name during a 20-season career at Gloucestershire between 1986 and 2005, including an innovative spell as captain of one of the best white-ball sides of the era.
In March 2009 he succeeded Clive Radley as head coach of the MCC, and latterly Marlborough College in Wiltshire. He has also served as assistant coach of the England Lions, including support roles with the senior white-ball squad, and assistant at Welsh Fire Men's team.
"I have always looked forward to travelling over the Bridge to the cricketing cauldron at Sophia Gardens or to a more relaxing holiday in North Wales - both done on numerous occasions," Alleyne said.
"My next trip though, as Glamorgan's white-ball head coach, will be my most anticipated. This unique splitting of the domestic roles - often reserved for International teams- tells me the club are serious about competing on all fronts.
"This is exactly the environment I love to be part of, and I can't wait to join Matt Maynard who will be leading the Championship challenge.
"Working in the white-ball coaching team with England in 2022 has given me the stimulus to make a big mark domestically. I am here unequivocally, to do just that."
Mark Wallace, Glamorgan's director of cricket, added: "We are absolutely thrilled to bring Mark on board as our white-ball head coach."
"Mark brings a wealth of experience to our white-ball sides and a fresh perspective on how we can move forward in both formats. It is an exciting time for the Club, and we are looking forward to Mark putting his stamp on our style of play.
"We want to compete across all formats, and with this new coaching setup, I am extremely optimistic about what the future holds for Glamorgan in both red-ball and white-ball cricket."