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The Mediterranean region is of fundamental importance to Europe given its strategic position. The responsibility for its overall ecosystem integrity is shared by European Union Member States (EU-MS) and other Mediterranean countries. A juxtaposition of overlapping governance instruments occurred recently in the region, with the implementation of both the Marine Strategy Framework Directive (MSFD) for EU-MS and the Ecosystem Approach Strategy (ECAP) for all Mediterranean countries, including EU-MS. Both MSFD and ECAP are structured around vision-driven processes to achieve Good Environmental Status and a Healthy Environment, respectively. These processes have clear ecosystem-based, integrated policy objectives to guarantee the preservation and integrity of Mediterranean marine ecosystem goods and services. However, adoption of these instruments, especially those related to the new EU-MS directives on marine policy, could result in a governance gap in addition to the well-known economic gap between the EU and the non-EU political blocs. We identify two complementary requirements for effective implementation of both MSFD and ECAP that could work together to reduce this gap, to ensure a better alignment between MSFD and ECAP and better planning for stakeholder engagement. These are key issues for the future success of these instruments in a Mediterranean region where discrepancies between societal and ecological objectives may pose a challenge to these processes.