This latest defeat for the Wanderers second string sees them remain adrift of fellow strugglers Leeds United and Wolverhampton Wanderers at the bottom of the FA Premier Reserve League table.
Chances came at both ends early on in the game as Bolton's Johann Smith headed a Michael Roddy free-kick wide of David Knight's goal whilst at the other end home keeper Sam Ashton was alert to tip over an awkward shot which nearly gave Boro the lead.
The visitors did manage to force the lead on the quarter hour mark when Graham Owens volleyed the ball past Ashton but on reflection the Wanderers could count themselves unlucky to be behind.
American forward Smith wasted a couple of good chances to bring Bolton back on level terms and this was to prove costly on 42 minutes when Tom Craddock added a second Middlesbrough goal.
Smith did finally manage to get the ball into the back of the Middlesbrough net just before the break but the linesman was to rule out the effort due to offside much to the anguish of the home side who had worked hard.
The early period of the second half saw Bolton reduce the errears as defender Bradley Hill scrambled the ball past Knight on 53 minures after some good work by team mate Dale Whitehead.
Middlesbrough wrapped up the victory on the hour when England U-19 winger Adam Johnson lashed a shot into the top corner to condemn Wanderers to yet another defeat at this level.
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