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Thomson, who won gold at the Commonwealth Games in Kuala Lumpur, Malaysia in 1998 in the men's 40km points race, is closing down his shop, Cycle Surgery Invercargill, which he has owned and operated in Tay St for the past 14 years.
Thomson said he considered himself "pretty lucky" to have an opportunity to work for Cycle Southland.
"It's a chance to do what I like doing. Cycling Southland have some awesome events."
His new role at Cycling Southland would be more than simply being involved in the big racing events, and would include going to schools and being involved in youth events.
He said another matter that he hoped he could help address was the level of accidents between cars and cyclists.
Cycling Southland general manager Nicola Wills confirmed the appointment.
"We are absolutely thrilled to have him on board. It is great to have someone like Glen with his background and knowledge with us."
While many fans were sad at hearing the news of his shop's closure, many also believed he was the right man for the job and wished him well on the shop's Facebook page.