The 26-year-old former Everton trainee made 29 appearances for the Shakers this term, scoring the in their season-opening Capital One Cup defeat to Middlesbrough.
"Mark is a high calibre player," said Stanley manager Leam Richardson in a club statement. "He's got experience, he's been at some good clubs and he's a good powerful defender."
Bury have inserted a 24-hour recall clause into Hughes' deal at the Store First Stadium.
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