Marquis was recalled following two starts with Double-A New Britain to get ready for the season after missing two weeks of Spring Training to tend to his 7-year-old daughter, Reese, who was seriously injured in a bicycle accident in Staten Island.
Hughes, 27, was the odd man out, as he didn't see much playing time despite a strong showing during Spring Training. He appeared in just four games, hitting .200 with two RBIs while seeing time at second base, third base and first base.
The Twins have 10 days to trade Hughes, release him or pass him through waivers. If he goes through waivers unclaimed, he could be optioned to Triple-A Rochester.
"We needed to carry 13 pitchers and we had a couple decisions to make, and this is the decision we made," said Twins general manager Terry Ryan. "I'm not going to get into individuals and playing one guy against another, because it's not fair to him or other players. It's just the decision we came to."
Hughes played in 96 games with the Twins last season, hitting .223 with seven homers, 12 doubles and 24 walks in 317 plate appearances. He said he was surprised by the decision and is looking to get a chance with another club.
"I hope to stay in the big leagues," Hughes said. "Hopefully some team values what I do and that I get an opportunity to go out and play. If that doesn't happen, we'll have to go through the process of what to do. Do I want to be back here again? I have no idea. I haven't really thought about it. Fingers crossed, someone values what I can do and I can go out there and play. Obviously the next few days will be interesting. I guess it's a waiting game now."
Hughes, a native of Australia, was signed by the Twins in 2002 as an amateur free agent. He's a career .224 hitter with eight homers and 33 RBIs in 102 Major League games and a career .268 hitter with 60 homers and 316 RBIs in 628 Minor League games.