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The waters of the United Arab Emirates (UAE) host a diversity of marine and coastal habitats that are under increasing pressure from multiple anthropogenic activities related to rapid economic growth. In response, Marine Protected Areas (MPAs) currently cover 12% of the UAE’s coastal and marine zones. The UAE National Biodiversity Strategy and Action Plan aims to increase the extent of protection to 14% by 2021, a target that exceeds current global commitments. We applied systematic conservation planning to (1) assess whether conservation features (i.e. species and habitats of conservation concern) are adequately represented in the current system of MPAs, and (2) identify complementary coastal and marine priority areas for conservation and management. Eight planning scenarios were produced based on different conservation targets, the inclusion (or not) of existing MPAs in the generated solutions, and the consideration (or not) of dredging (an activity linked with coastal development in the UAE). A gap analysis demonstrated that to achieve the targets set by experts for all conservation features, additional areas would need to be integrated in conservation plans and policies. Key coastal and marine priority areas were consistently selected for conservation across all planning scenarios. The findings of this work provide a basis for the identification of conservation priorities that can be embedded in the current network of MPAs by extending their boundaries, in post-2020 conservation strategies including plans for creating new MPAs, and in broader spatial planning initiatives.