Aim: As a step towards providing support for an ecological approach to strengthening marine protected areas (MPAs) and meeting international commitments, this study combines cumulative impact assessment and conservation planning approach to undertake a large‐scale spatial prioritization.Location: Exclusive Economic Zone (EEZ) of Brazil, Southwest Atlantic Ocean.Methods: We developed a prioritization approach to protecting different habitat types, threatened species ranges and ecological connectivity, while also mitigating the impacts of multiple threats on biodiversity. When identifying priorities for conservation, we accounted for the co‐occurrence of 24 human threats and the distribution of 161 marine habitats and 143 threatened species, as well as their associated vulnerabilities. Additionally, we compared our conservation priorities with MPAs proposed by local stakeholders.Results: We show that impacts to habitats and species are widespread and identify hot spots of cumulative impacts on inshore and offshore areas. Industrial fisheries, climate change and land‐based activities were the most severe threats to biodiversity. The highest priorities were mostly found towards the coast due to the high cumulative impacts found in nearshore areas. As expected, our systematic approach showed a better performance on selecting priority sites when compared to the MPAs proposed by local stakeholders without a typical conservation planning exercise, increasing the existing coverage of MPAs by only 7.9%. However, we found that proposed MPAs still provide some opportunities to protect areas facing high levels of threats.Main conclusions: The study presents a blueprint of how to embrace a comprehensive ecological approach when identifying strategic priorities for conservation. We advocate protecting these crucial areas from degradation in emerging conservation efforts is key to maintain their biodiversity value.

Current methods in conservation planning for promoting the persistence of biodiversity typically focus on either representing species geographic distributions or maintaining connectivity between reserves, but rarely both, and take a focal species, rather than a multispecies, approach. Here, we link prioritization methods with population models to explore the impact of integrating both representation and connectivity into conservation planning for species persistence. Using data on 288 Mediterranean fish species with varying conservation requirements, we show that: (1) considering both representation and connectivity objectives provides the best strategy for enhanced biodiversity persistence and (2) connectivity objectives were fundamental to enhancing persistence of small‐ranged species, which are most in need of conservation, while the representation objective benefited only wide‐ranging species. Our approach provides a more comprehensive appraisal of planning applications than approaches focusing on either representation or connectivity, and will hopefully contribute to build more effective reserve networks for the persistence of biodiversity.