The defender is the club's longest-serving player - having made his debut in 2001 - but has extended his stay at the Britannia Stadium, with the option of a further 12 months
The 29-year-old is the club's longest-serving current player, having made his debut in 2001, and also agreed an option for a further 12 months as part of the deal.
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"Everyone knows how much the club means to Andy – he's Stoke City through and through," Hughes told the club's official website.
"He didn't play as many games last season as he would have hoped but he's determined to force his way back into the side on a regular basis and still has a part to play going forward."
The club's chief executive Tony Scholes added: "Andy has given the club fantastic service and was a key figure in our promotion from the Championship and helping us to become established in the Premier League.
"We're delighted we have been able to reach an agreement with him over a new contract."