The Latics took the lead on four minutes through Hughes. There appeared to be little danger when strike partner Craig Davies' header found him on the edge of the box.
But Hughes turned Adam Barrett before blasting the ball past Southend goalkeeper Steve Collis.
The hosts should have equalised four minutes later when skipper Kevin Maher fed Leon Clarke and he rounded Oldham keeper Mark Crossley only to shoot wide with the goal at his mercy.
Davies forced a smart parry from Collis before Barrett saw his header nodded off the line by Ryan Bertrand.
The match continued to be an end-to-end affair with Crossley saving from Maher before Dean Morgan saw his shot saved by the stopper from a cross-field Lewis Hunt cross.
At the other end of the field Collis saved from Davies and turned a 25-yard Neil Kilkenny shot wide of his right post.
After the break Crossley kept Oldham in front by producing two decent saves to deny Leon Clarke.
And the Latics were denied a good shout for a penalty after Peter Clarke handled the ball, while Hughes saw his goalbound shot deflected out for a corner.
Southend were reduced to ten men in the 73rd minute when Alan McCormack was sent off for his second bookable offence.
But Steve Hammell was denied a chance to equalise when his 35-yard free-kick was palmed out by the impressive Crossley.
The win was Oldham's fifth on the spin on the road and extended their unbeaten run to ten games.