Moses, on loan from Chelsea, suffered a hamstring injury during Stoke's 1-1 Premier League draw at West Ham last weekend.
Hughes told the club's official website: "It may well be that Victor's season is over unfortunately because of the type of injury he has got. He might get back but at the moment we're probably thinking that he won't make it.
"It's a shame because Victor has done really well since he's been with us.
"He was our shining light in the early part of the season and then unfortunately he got a couple of quite serious injuries that held him back and in the end he hasn't been able to finish the season with us.
"He'll look back on his time with us and think he's made an impression and done well and we'd agree with that because he's been a really important figure for us this season."
'People will remember us because we got to No.1 in the world rankings and achieved great things - but our biggest regret is that we didn’t win anything': Ex-Everton star Kevin Mirallas opens up on 'honour' of being part of nation's golden generation
‘I’m sure we’d have finished in the top four or five if he hadn’t joined Chelsea in January. Him leaving damaged the team, but we couldn’t stand in his way’: Alan Curbishley reflects on failed Champions League dream after selling key player
