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Marine protected areas (MPAs) have a long history, originating in traditional and cultural initiatives often focused on reserving resources for food security. A handful of ‘parks’ were established between the 1870s and 1940s and, following World War II, increased awareness of threats to the ocean led to global programmes that started in the 1970–1980s. Initially IUCN became the leader, piloting a science-based ‘critical marine habitats’ approach, by which MPAs were aimed at conserving the healthiest and most diverse ecosystems, endangered and charismatic species, and high-profile habitats. During the 1970s, with the support of WWF, UNESCO, UNEP, and growing national efforts, the MPA concept evolved to include biosphere reserves, marine reserves and sanctuaries, large ocean reserves, and other designations that aimed to reconcile long-term protection with human use. From the 1980s, MPAs greatly expanded in number and scope. By the turn of the millennium, MPAs were proliferating, and principles and methodologies were available to guide their establishment and management in a harmonized manner. Zoning for different uses was widespread, but questions were being raised about the efficacy of biodiversity conservation in areas where extractive uses were permitted. MPA implementation accelerated once targets were introduced by the Convention on Biological Diversity. Campaigns and fundraising by non-governmental organizations and further national efforts resulted in a rapid increase although, by 2015, less than 4% of ocean surface was protected. Current challenges include: (1) understanding the role of MPAs in maintaining ecosystem services, fishery management, climate change adaptation and mitigation, and other emergent problems; (2) more rigorous network design; (3) effective governance and demonstration of ‘success’; and (4) integrating MPAs with marine spatial planning. While MPAs have provided one of the most viable and politically acceptable approaches to marine conservation for 50 years, their role in developing a fully effective marine ecosystems management regime has yet to be fully explored and understood. Copyright © 2016 John Wiley & Sons, Ltd.

International audience; Overfishing and habitat destruction due to local and global threats are undermining fisheries, biodiversity, and the long-term sustainability of tropical marine ecosystems worldwide, including in the Coral Triangle. Well-designed and effectively managed marine reserve networks can reduce local threats, and contribute to achieving multiple objectives regarding fisheries management, biodiversity conservation and adaptation to changes in climate and ocean chemistry. Previous studies provided advice regarding ecological guidelines for designing marine reserves to achieve one or two of these objectives. While there are many similarities in these guidelines, there are key differences that provide conflicting advice. Thus, there is a need to provide integrated guidelines for practitioners who wish to design marine reserves to achieve all three objectives simultaneously. Scientific advances regarding fish connectivity and recovery rates, and climate and ocean change vulnerability, also necessitate refining advice for marine reserve design. Here we review ecological considerations for marine reserve design, and provide guidelines to achieve all three objectives simultaneously regarding: habitat representation; risk spreading; protecting critical, special and unique areas; reserve size, spacing, location, and duration; protecting climate resilient areas; and minimizing and avoiding threats. In addition to applying ecological guidelines, reserves must be designed to address social and governance considerations, and be integrated within broader fisheries and coastal management regimes.