The Imps deservedly took an early lead, but then allowed their county rivals back into the game. But Hughes' 59th minute strike inflicted defeat on an in-form Boston team which had only lost one of their previous seven games.
Lincoln were on top early on and Martin Gritton latched onto a pass from Scott Kerr in the second minute, but shot wide from a good position.
Then Lincoln's Jamie Forrester fought his way down the right flank and sent in a cross which needed a timely interception from Boston's centre-back Ian Miller to prevent Mark Stallard from scoring.
But Stallard got on the scoresheet in the 16th minute when the Boston defence failed to cut out a ball down the middle. Stallard beat the offside trap and calmly placed his shot past the helpless Andy Marriott.
Boston responded with a long-range effort from David Galbraith which went straight at keeper Alan Marriott. But Boston created a great chance in the 25th minute when Miller and Anthony Elding set up Francis Green, but the striker put his shot wide from close range.
Boston had a scare when Galbraith sent a powerful header over his own bar but they recovered to draw level in the 38th minute.
On-loan striker Dany N'Guessan headed on a free-kick for Jason Kennedy. The midfielder timed his run to perfection and finished with a volley which rocketed into the net off the underside of the bar.
Boston had their best spell early in the second half but were thrown when Lincoln introduced substitutes Lee Frecklington and Hughes in the 53rd minute switched from 4-3-3 to 4-4-2.
Almost immediately Ryan Amoo created an opening for Forrester but the striker mis-kicked from two yards out.
Lincoln got the winner when they broke away after clearing a Boston corner. Forrester cleverly held the ball up before his pass released Nicky Eaden.
The midfielder sent over a cross to the far post which Frecklington headed back for Hughes to fire home from close range.
Boston had a chance to equalise when Miller climbed above the Lincoln defence but sent his header straight at the keeper.
Ten minutes from time Forrester almost got a third goal for Lincoln but was denied by the post.