The Linnets reached the National League North play-offs last season but the new campaign is off to a slow start.
Winning just one of their first ten matches, the club sit third from bottom of the table - a far cry from last year when they were in the title races until the final stages.
The manager stepped in when Tommy Widdrington left to join Aldershot Town in April.
Hughes and number two Adrian Whitbread have left the Walks and chairman Stephen Cleeve says he is sad things have not worked out.
He told the club’s website: “I will always be grateful to Mark for stepping up to the plate when Tommy Widdrington walked out on the club without notice to join Aldershot. Mark is a tremendous person and gave his all to the job in trying circumstances.
“I am very sad that it has not worked out as we both wanted at King’s Lynn Town. I wish him well in his future career and am sure he will bounce back very quickly.”
IMAGE CREDIT - IAN BURT