Shares at the UK cidermaker fell sharply on Monday when it warned of "previously unidentified promotional costs" of some £3.3m.
Bulmer said the costs came to light after a change in the management team at its off-trade business, dealing with supermarkets, off-licences and cash and carry outlets. And blamed the bad news on "administrative indiscipline".
Bulmer's chairman Will Samuel said the board had lost confidence in Hughes. His resignation was accepted ahead of the company's agm on Wednesday, which was postponed while the search for a new chief executive gets under way.
In the meantime, Colin Brown, a non-executive director, will take charge.
In July Bulmer said it would cut back its overseas operations and focus on the UK due to fierce competition from ready-to-drink products such as Smirnoff Ice.
Bulmer confirmed that restructuring at its US business had significantly reduced losses, and that performance of key brands Strongbow cider and San Miguel beer was â€œahead of the market.
For the year ended April 26 sales at Bulmer rose 11% to £585m. But pre-tax profit fell 26% to £21m.