There was a suggestion Mills could join initially on a season-long loan, but the centre-half has signed a three-year deal after the clubs agreed an undisclosed fee.
He is Wanderers' second close-season signing following the arrival of free agent Keith Andrews.
Bolton manager Owen Coyle said: "Matt is a player who has a high level of experience in the Championship.
"We are delighted to have made this acquisition as he adds strength and quality into the mix.
"He is 25 years old and has already captained teams at this level, so we know what he will bring to the squad, both on and off the pitch."
Bayern Munich are kings of Germany and hope to be crowned kings of Europe at Wembley later this month!
Borussia Dortmund hears Wembley Calling and are headed to London for the Champions League final.
Chelsea won the Europa League on Wednesday. The Blues defeated Benfica 2-1 on injury time goal from Ivanovic.
The Juventus jersey for the 2013/14 was released earlier this week. Be the first to wear the colors of the Old Lady.
The adidas Nitrocharge is the most talked about new cleat in years. It was released on May 15 and will take your pitch by storm.
adidas has added some color to the Predator line with this new colorway. Released on May 17. Be the first to own a pair.
The Liverpool 2013/14 soccer jersey is available for pre-order. The Reds are eager to compete for silver next season.
The push for more color on their cleats, adidas has added the infrared colorway to the adiZero f50 Line.
The new PUMA evoSPEED 1.2 FG. A great new soccer cleat with classic look and first time for PUMA to be on the cleat.
One of the top soccer cleats for control the Nike CTR360 will not let you down on the field in tight spaces.