Complex coral reefs offer hope for management in a Marine Protected Area in Zanzibar

Management of Marine Protected Areas can be supported by a detailed understanding of ecosystem state. We assessed coral reefs within Pemba Channel Conservation Area in 2019 and evaluated changes over the previous decade. In 2019, hard coral cover ranged from 3.5 % to 58.4 % across sites, while coral recruitment was exceptionally high in places (14 recruits/m2). The highest total fish biomass was ∼ 500 kg/ha, which is low compared to forereefs elsewhere in the Western Indian Ocean. Between 2009 and 2019, benthic substrate shifted to higher soft coral and turf algae cover, and mean fish density significantly decreased. This suggests that overfishing is a major threat and some reefs will require restoration to facilitate recovery. However, Pemba's unique geomorphology might offer refuge for corals from future warming and habitat for large, endangered fishes such as groupers. This could elevate the global significance of Pemba's reefs and should motivate investment in management and conservation of these resources. •Evidence is required to support management of Marine Protected Areas.•Fish populations at reefs in Pemba Channel Conservation Area are low compared to elsewhere in the Western Indian Ocean.•Coral reef condition has declined between 2009 and 2019.•Pemba's unique and complex reef structure offers a potential refuge for corals from future warming and habitat for endangered fishes.