Hughes, who previously worked for M&S, Pret, Eat and Paddy Power, had "overall responsibility for retail operating standards and processes, levels of customer service as well as the motivation and engagement of 5,000+ staff".
Wyevale said: "We can confirm that Colin Hughes will be moving on from his role as Retail & Operations Director with Wyevale Garden Centres. We thank Colin for his significant contribution to the business over the last three and a half years and wish him well for the future. We will announce his replacement in due course."
Wyevale's head of buying horticulture and gardening Caroline Linger also left this month as changes brought in under new chief executive Roger Mclaughlan and new chairman Justin King start to be felt. There is no plan to replace Linger.
Wyevale held a telecon on 20 October to update senior staff about changes in management.
Wyevale issued a report for a "challenging year" in July 2016.
Mclaughlan replaced Kevin Bradshaw in March 2016, King replaced Stephen Murphy in August 2016, Paul Emslie replaced trading director Dan Zinner in May 2016, when supply chain director Richard Morgan came in and multichannel director Tim Patten left.