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Abstract: Marine protected areas (MPAs) are often managed using several management zones, each of which allows different human-uses. Decision support tools can be applied to provide advice on potential zoning configurations. However, few studies used decision support tools to systematically determine good locations for different types of zones that accommodate multiple and often conflicting objectives. Previous studies have mostly used scores to integrate multiple objectives and identify different zoning configurations or explored priority areas for each zone separately. Neither of these approaches ensure that solutions meet both biodiversity and human-use objectives. Nor do they deal with the fact that in zoning plans the whole is not the same as the sum of the parts, the importance of a site depends on how the rest of the sites are managed. The aim of this study was to identify different zoning configurations for the Raja Ampat MPA network in Eastern Indonesia that address biodiversity, sustainable fisheries and community resource access objectives. Identifying zoning configurations is particularly difficult here given the importance of protecting high biodiversity reefs and other conservation values, and the high reliance of local communities on their marine resources. Potential areas for no-take zones were identified that have a small and equitable impact across the fishing grounds of different fishing communities whilst ensuring each community has access to a ‘sustainable fishing zone’. Access to fishing grounds for each community is complicated due to marine tenure restricting where individuals can fish and reliance on traditional types of fishing vessels that restrict long distance travel. This approach for zoning was compared to three others. The first focused on identifying areas only for the no-take zone, a traditional systematic planning approach, and the second on both zones without explicitly accounting for the issue of resource access for each community. The solutions unfairly impacted particular communities. Finally, it is demonstrated how a pre-existing zoning proposal, driven by negotiation can be integrated into systematic planning. [Copyright &y& Elsevier]