21-year-old Hughes joined the club in the summer of 2013 as part of the Elite Development Programme and has been on good form for Stirling County in the RBS Premiership.
After starting on the wing against Toulon in the Heineken Cup last month, Niko Matawalu moves to full-back.
Richie Vernon starts his first game at centre, since switching positions from the backrow, and will partner Mark Bennett in midfield.
Ruaridh Jackson has been released from the Scotland squad and starts at fly-half, with Henry Pyrgos wearing the No 9 jersey, after signing a new one-year deal with the club this week.
Gordon Reid starts at loose-head and Ed Kalman is at tight-head, while Pat MacArthur also comes back from Scotland duty and takes his place at hooker.
Leone Nakarawa and Tom Ryder are in the engine room, with Rob Harley at blindside and Tyrone Holmes at openside. Josh Strauss returns to the side after missing the Toulon game through injury and will captain the team at number 8.
Former Warriors Elite Development scrum-half, Murray McConnell is named amongst the replacements, having been in great form for his club side Ayr this season.
Glasgow Warriors head coach Gregor Townsend said: "Connacht are an extremely tough side to play and it was a very close game when we played them in over in Galway in November, so we know we face a real challenge on Sunday.
"International call-ups and injuries during this period of games shows how important it is to put together a strong squad with real depth.
"Last season during the RBS 6 Nations our players stepped up and performed really well, so we expect those involved on Sunday to seize their opportunity.
"We were delighted to get Lee Jones in this week and he is a player who has impressed in the international set up and is a proven try scorer. He gets an early opportunity to play for the club and it's a great chance for him to do what he does best in front of our home supporters.
"Rory Hughes has impressed all season in training and has come close to playing a few times. He's worked hard on his game and performed well for Stirling County, so we're looking forward to seeing him in a Warriors jersey.
"We've been keeping an eye on a number of young Scottish club players and Murray McConnell is one who has been working extremely hard and fully deserves to be involved this weekend."
Tickets for the game against Connacht at Scotstoun Stadium this Sunday (kick-off 2pm) are available from www.glasgowwarriors.org and from the ticket office on 0844 800 3490 (Monday to Friday, 9am-5pm). Tickets will also be available from the Murrayfield ticket office on Saturday. The ticket office at Scotstoun Stadium will be open from 10.30am on Sunday and tickets will be available to purchase right up until kick-off.
Glasgow Warriors team to play Connacht, RaboDirect PRO12, Scotstoun Stadium, Sunday 9 February (kick-off 2pm):
15. Niko Matawalu
14. Lee Jones
13. Richie Vernon
12. Mark Bennett
11. Rory Hughes
10. Ruaridh Jackson
9. Henry Pyrgos
1. Gordon Reid
2. Pat MacArthur
3. Ed Kalman
4. Leone Nakarawa
5. Tom Ryder
6. Rob Harley
7. Tyrone Holmes
8. Josh Strauss (Captain)
Substitutes
16. Dougie Hall
17. Jerry Yanuyanutawa
18. Jon Welsh
19. James Eddie
20. Fraser Brown
21. Murray McConnell
22. Finn Russell
23. Scott Wight
Not available due to injury: Mike Cusack (shoulder), Peter Horne (knee), Al Kellock (arm), Byron McGuigan (hand), Sean Maitland (head/knee/ankle), Peter Murchie (shoulder) and DTH van der Merwe (shoulder).
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