Goals from Cesc Fabregas and Fran Merida ensured that the Gunners continued their unbeaten run in the league and also their recent run of results over a club once considered to be their bogey team.
Bolton had been hoping to give new manager Owen Coyle a winning start in his first game since joining the club from Burnley.
And the new manager resisted the temptation to tinker with the starting line-up, naming the same 11 that had surrendered a two-goal lead to Hull City in Gary Megson's last game in charge.
Arsene Wenger brought back Cesc Fabregas into the heart of his midfield and gave Londoner Craig Eastmond his first full start for the Gunners.
However, there was no place in the squad for Sol Campbell, who joined the club on a free transfer earlier in the week.
Bolton had the better of the earlier exchanges and would have handed their new manager a dream start inside two minutes if Kevin Davies had been able to get his shot away inside the six-yard box after picking up on Chung-Yong Lee's cross.
Ivan Klasnic also saw a goal ruled out for offside, but the Gunners soon got into gear and with Fabregas pulling the strings in midfield.
The Spain international played Eduardo in on goal, causing Jussi Jaaskelainen to rush off his line to make a well-timed intervention.
But moments later, it was Fabregas himself who was sent tumbling to the floor for what looked a stonewalled penalty only for referee Phil Dowd to indicate otherwise.
Arsenal made the breakthrough on 28 minutes and, predictably, it was Fabregas again who did the damage, firing into the bottom corner after playing a neat one-two with Eduardo.
Bolton made sure the visitors didn't have it all their own way and went close to an equaliser when Lee and Gretar Steinsson both tried their luck from the edge of the box.
But Arsenal remained dangerous on the break and Fabregas should have made it two after getting on the end of Andrey Arshavin's low cross from the left.
Klasnic also went close for the home side just before half time, turning William Gallas inside the area before producing a weak shot that failed to beat Manuel Almunia.
Backed by the biggest gate at the Reebok this season, Bolton made a confident start to the second half.
Lee put in a number of dangerous crosses and Matt Taylor wasted two glorious opportunities to level the scores.
But Arsenal put the game to bed on 78 minutes when Fabregas burst through the middle and squared for Eduardo, whose cross was turned in at the far post by Merida.