The 26-year-old centre-back, who was released by the Shakers after two seasons at Gigg Lane, has put pen to paper on a two-year contract at the Globe Arena.
Morecambe manager Jim Bentley has immediately made Hughes his new captain.
"Mark is a player I have always kept an eye on and I delighted that he has signed for us," Bentley told the club's official website.
"He has a lot of qualities and is a great talker as well as a good defender and will be an excellent captain for us."
Hughes is likely to make his debut in tonight's friendly against Burnley.