The 26-year-old former Everton trainee made 29 appearances for the Shakers this term, scoring 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.
"That experience is what we've been looking to add to the defence, the squad and the back four. He's very similar to Nicky Hunt in that one of the big plusses is that he wants to come and play for the club.
"I only had to ask the lad once and he was more or less in the car straight away."
Hughes is Accrington's third piece of business on transfer deadline day following Paul Rachubka's return on loan from Leeds and the extension of Rotherham defender Hunt's stay at the Store First Stadium.