Ellison has been with the club for almost 10 years, having joined as a player in 2011, and then taking up the manager’s role in 2016.
A club statement said: “The Runcorn Linnets Board have decided not to continue the partnership between the club and the Management Team of Michael Ellison and Matthew Cross.
"Discussions regarding next season, and the future of the club revealed differences in approach that ultimately proved to be incompatible.”
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