The 26-year-old centre-half, who joined Bolton in January 2011, will now stay at the Reebok Stadium until 2016.
"I'm very happy to have signed," Wheater told the club's official website.
"I believe we have a real chance to move forward this season and the manager is certainly the right man for us.
"I also believe he can help get the best out of me as a player.
"I'm also very happy living in the area and have made lots of new friends since moving here from Middlesbrough."
- Sports & Recreation