Experienced Hughes, who was appointed in the summer to lead a new-look Robins squad in the SCFL Division 2 - advised chairman Neil Redman of his decision to resign earlier 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."
Bosham lost all three league matches under Hughes, conceding nine times and scoring a solitary goal.
Tony Hancock and Danny Mullen, part of Hughes' management team, are set to take caretaker charge for the foreseeable future.
Robins will be looking to register their first points as they welcome Worthing Town on Saturday.
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