The third round was played in a steady rain. However, lift-clean-and-place rules were not in effect. Action was halted for 30 minutes late in the round due to water puddling on the greens.
'I'll take under-par on a day like this,' Hughes stated. 'You just have to be patient because you know it is going to be the same for everyone. I've had a bit of experience playing in conditions like this.'
Chris Baryla (67) and 2000 U.S. Amateur champion Jeff Quinney (69) are tied for second place at 8-under-par 205. Gavin Coles, who briefly held the lead early in round three, carded a 3-under 68 and is alone in fourth at minus-7.
Boo Weekley shot 69 for the second straight round and is in fifth at 5-under-par 208.
Hughes, who owns four straight top-25 finishes since missing the cut at the British Open, stumbled to a double-bogey on the first. That dropped him to minus-7.
Coles birdied the first, then ran off three straight birdies from the fourth to jump to minus-8 and into the lead at StoneWater Golf Club.
The 39-year-old Hughes got one of those strokes back with a birdie on the fourth. He got back to minus-9 thanks to a birdie on the par-3 sixth. That gave him the lead as Coles had dropped a stroke on No. 9.
Hughes parred four straight from the seventh before a bogey on the 11th dropped him to minus-8 and into a share of the lead with Quinney. Hughes birdied the 13th to regain the outright lead.
Before Hughes' group putted on the 15th, the weather delay halted action. The last few greens were gathering plenty of water from the rain and puddles were making some of the greens unplayable.
When players returned to the course, Hughes pushed his lead to two shots with a birdie on 17 and he parred the last to remain two ahead.
'I didn't really have any close putts today,' admitted Hughes, whose lone tour win came at the 2004 Wichita Open. 'But I was happy with my long approach putts.'
Quinney dropped in a 14-foot birdie putt on eight and gained a share of the lead with his birdie effort on 11. He parred his next three then birdied the 15th to briefly tie Hughes for the lead.
The former U.S. Amateur champion stumbled to a bogey on the 16th before carding pars on the final two holes.
'It was a long day. The weather was tough with the wind and the rain,' Quinney explained. 'I wasn't swinging it great, but I'm happy with the end result.'
Baryla, a Monday qualifier, flew up the leaderboard with three birdies over a four-hole span from the fourth. He dropped a stroke on eight, but atoned for the mistake with a birdie on 10. Baryla bogeyed the 11th to slip to minus-6. He climbed into a share of second with birdies on 16 and 17.
Cameron Beckman is alone in sixth place at 4-under-par 209 after a 72 on Saturday. Ricky Barnes, the 2002 U.S. Amateur champion, was joined in a share of seventh place by Josh Broadaway, Akio Sadakata, Scott Gardiner, Craig Lile and Jarrod Lyle.