Hughes, who made 38 league appearances this season, was an integral part of the side that won promotion to the Championship.
Simon Grayson told the club website: "He played in a number of different positions and he will be an asset to our squad next season."
The 32-year-old joined Leeds in the summer of 2007 from Norwich and has featured in 126 games.
Hughes signed for the club on the same day Leeds' 15 point deduction was confirmed following their relegation to from the Championship.
He is one of only four players left at Elland Road from the team that lined up for Leeds' first ever League One game at Tranmere.
Source: BBC Sport
Source: BBC Sport