This study assessed the Zanzibar sea cucumber fishery using a multidisciplinary approach. Data was collected by (i) interviewing various groups of actors in the fishery and reviewing management documentation and legislation, (ii) by monitoring catches and (iii) through a visual census of coastal sea cucumber populations in areas open and closed to fishing. The fishery showed clear signs of being unsustainable with high fishing effort, and weak formal and informal management institutions. The fishery operation was characterised by an intricate cross-scale structure with both fishers and sea cucumber products being transported across national borders. The visual census of commercial sea cucumber stocks at three sites open to fishing around Zanzibar showed low densities across the range of sea cucumber value groups including low value species. Furthermore, the diversity of commercial sea cucumber species was lower in fished reefs than on a protected reef. The poor status of the sea cucumber populations was confirmed by the perception of an overfished resource by the interviewed actors active in the fishery. This was also depicted by the paucity of high value species, and high representation of low value and newly commercialised species in fishers catch. We conclude that the current state of Zanzibar’s sea cucumber populations is compromising the fisheries self-replenishment and existence and that the fishery is in urgent need of a complete management reform.