The Saints earned themselves a place in the final four of the competition with a 2-0 quarter-final victory over the League One high-flyers at the DW Stadium.
Southampton are currently fighting relegation from the Premier League but new manager Hughes was impressed with both the quality of his players and their performances in his maiden game.
"It was an important day for the players today," Hughes told BBC Sport after the game.
"I have been really impressed with the quality of the talent I have. They have lost a bit of confidence recently but they are good players.
"We stood up to Wigan. It was a statement of intent and a start. We have work to do in the Premier League, but we will enjoy this moment.
"We did not create enough in the first half, but we were resolute throughout and made the right decisions in the key moments."
Saints are in the final four of the FA Cup alongside Manchester United, Tottenham Hotspur, and the winner of Sunday's game between Leicester City and Chelsea.