Hughes, working his way back from velocity and arm issues, struck out eight and held New Hampshire to a run on three hits and two walks in Trenton's 3-2 win at Waterfront Park. The right-hander said he pitched "much better" on Wednesday, his start coming in front of Yankees general manager Brian Cashman and team executives Mark Newman and Reggie Jackson.
He was clocked as high as 94 mph on ballpark radar guns and left to a standing ovation in the seventh after reaching his pitch count.
"I felt comfortable out there and my mechanics were in sync," Hughes told MLB.com. "I wasn't perfect by any means today, but I was throwing a lot more strikes than last time out, and that was a positive sign."
Hughes' only run allowed came after he departed in the seventh, when New Hampshire's Ricardo Nanita hit a ground-rule double off Trenton reliever Cory Arbiso to knock home Travis d'Arnaud.
Hughes didn't give up a hit until the fourth, when New Hampshire center fielder Anthony Gose singled to right.
"[My comfort level] was much better, I felt like I was throwing more strikes today," said Hughes, who went on the DL on April 19 with the team called right shoulder inflammation. "Until the end, I was commanding the baseball pretty well."
Hughes, 25, was throwing consistently around 93 mph, according to MLB.com, a promising sign for the 2010 American League All-Star who dealt with decreased velocity this spring. He was 0-1 with a 13.94 ERA in three starts with New York this year before going on the 15-Day disabled list.
"I made them swing the bat. I didn't want to fall into deep counts, and I wanted to make sure I faced a lot of hitters and went deep into the game," Hughes said. "My last two outings, stuff-wise, have been good. It was the command that faltered a little bit. I didn't necessarily think about what the radar gun said after every pitch."
Hughes threw 88 pitches in the outing -- his limit entering the day was 85-90, according Trenton manager Tony Franklin. He threw 61 strikes and retired the first 11 batters he faced.
"From what I've heard, [I'll make] one more [rehab start]," Hughes said. "But I'll have to show that I'm ready to go after that."
That start could come on Independence Day with Triple-A Scranton/Wilkes-Barre, which will host Lehigh Valley on Monday.
The Yankees have missed Hughes' consistency in their rotation, especially after losing Bartolo Colon for several weeks. Cashman signed former Phillies Minor Leaguer Brian Gordon earlier this month to make a few spot starts as Hughes worked on his mechanics.
Hughes has responded well since beginning his rehab. He struck out seven over 4 1/3 innings in his first outing with Class A Short-Season Staten Island on June 19 before throwing 72 pitches in 3 1/3 innings in his second start last Friday with the Thunder.
"The last inning, I may have fatigued a little bit. I felt like I was a little late. I don't know if it was mechanical -- I didn't feel tired -- but I may have yanked a couple cutters and my command wasn't as crisp," Hughes said.
"I felt like I was able to let the ball go, and it was free and easy," he added. "I've felt that way since I got the cortisone and rest."
Hughes received a cortisone injection in his right shoulder April 28.