Assistant boss leaves the club.
Dunne appointed his fellow Irishman as soon as he was named Colchester United boss in September 2012 and the pair have worked closely together for the past couple of years.
Their time at the Weston Homes Community stadium has now come to an end but Chairman Robbie Cowling said: "We would like to sincerely thank Mark for his hard work here.
"To some people, the last two years have been a struggle for Joe and Mark, but they have done a tremendous job in securing our League One status for the past two seasons."
"As earlier with Joe, I would like to wish Mark the best of luck for the future."