The Brighton boss is the only BAME manager currently in the Premier League, while across the football leagues they are still hugely under-represented, especially when considered the diversity of players in the leagues.
The issue has again hit the headlines after the appointment of former Arsenal and England defender Sol Campbell to the manager's position at Macclesfield in League Two, but Hughton thinks there is still a long way to go.
"At this stage of our game the fact that there are not more black and ethnic managers at higher levels is the biggest challenge that black coaches have," said Hughton.
"I still see that as a challenge and we can look at particular individuals and I might know lots of the circumstances around that individual or not.
"But I would speak from a broader point of view, the general rather than the individual, and there are still challenges ahead.
"As someone who has campaigned and pushed and seen developments, with FA initiatives, and the work others are trying, firstly I'm delighted to see another black manager [Campbell] going into a very difficult job."