Hughes - who was appointed to the role in the summer to lead a new-look squad in the Southern Combination Division Two - advised Chairman, Neil Redman of his resignation this week.
Redman said: "We would like to thank Dennis for his efforts during his short time at the club, and wish him well.
"We have been looking for stability over the summer and thought that with Dennis' experience it would help achieve that, but for various reasons he has decided it's not working out for him, and was honest enough to tell me."
It has been a challenging opening couple of weeks for the side, with three successive defeats away at Roffey (1-2), Jarvis Brook (0-5) and Angmering Seniors (0-2).
Hughes' management team included Tony Hancock and Danny Mullen - who shall take caretaker charge for the foreseeable - as the club seeks its first points at Saturday's opening home fixture of the season, against Worthing Town (3pm).