But it was the form of keeper Mark Bunn that was crucial as Cobblers kept a clean sheet for the third match in a row as they leap-frogged Brighton.
Bunn pulled off several outstanding saves to keep Northampton in the contest early on and then preserve all three points in the second half as Brighton threatened an equaliser.
The Town keeper was soon in action, making a double save to keep out a header from Nathan Elder and then quickly foil top scorer Nicky Forster from the rebound.
Bunn then raced out to deny Forster after he broke through before producing a reflex save to keep out a close-range header from David Martot.
Forster should have broken a deadlock in the 26th minute when he struck the bar from close range and then shot over after catching Northampton asleep with a free-kick.
Northampton gradually got into contest as the half wore on. Ryan Gilligan headed over from a Poul Hubertz cross and Matt Richards cleared off the line to deny Brett Johnson.
Town broke the deadlock in the 44th minute when Danny Jackman's free-kick was headed home at the far post by Hughes.
Hubertz should have added a second 12 minutes after the restart but he could only head over from Jackman's pin-point cross.
Hughes almost grabbed his second goal of the game just after the hour, but he could only head over from Jackman's corner.
Brighton threatened late on and it took another excellent save from Bunn to keep out a Richards free-kick which came through a crowd of players.
Substitute Ian Henderson should have sealed the points from a quick breakaway, but he lacked composure with only keeper Michels Kuipers to beat.