Indonesian coral reefs are under pressure from illegal, unregulated and unreported fishing, the use of destructive fishing practices, land-based pollution, coastal development and climate change. Marine protected areas (MPAs) are necessary to allow habitat recovery and fish stock replenishment. Through the United States Agency for International Development Sustainable Ecosystems Advanced Project (2016–2021), Indonesia worked to improve fisheries productivity and sustainable livelihoods within the three provinces of Maluku, North Maluku and West Papua, where 13 new coral reef MPAs were designed for multiple use, with a zoning system to support biodiversity conservation and sustainable fisheries. At the time of writing in mid-2021, regulations to prohibit fishing within the no-take areas (NTAs) were not yet implemented. This paper presents baseline and trends in percent coral cover and reef fish density and biomass in the MPAs. In 2020, overall coral cover had increased from 42% to 45% across all MPAs. The average target fish biomass across all NTAs had declined from 1709 ( ± 176 SE) kg per hectare in 2017 to 884 ( ± 76 SE) kg per hectare in 2020, representing a significant decline of about 48%. Large and significant declines in many target fish families across multiple MPAs are reflective of unsustainable levels of exploitation. It is evident that management plans need to be implemented with adequate enforcement and stakeholder engagement to stem the decline of target species and to secure livelihoods for local fishing communities.
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