“Mark brought the squad together during the closing stretch of the season and gave us a fighting chance,” chairman Tom Piatak added.
“His leadership, composure, and connection with the players was clear, and we’re confident in his ability to lead us forward.”
Despite their relegation, Hughes reinvigorated his side for the end-of-season run-in as they lost just once at home under his tenure and won three consecutive games for the first time in more than two years.
A run of 10 points from four games in April came too late to pull them out of trouble, however, with Hughes wanting to remain in post despite the drop into non-league football.