New EU policy initiatives within the Maritime Strategy Framework Directive, the Integrated Maritime Policy, the reform of the Common Fisheries Policy, the offshore Energy policy and the Blue Growth Strategy, are in different manners aiming at implementing Ecosystem Based Management (EBM). EBM focuses on regional areas, as opposed to traditional sectoral driven policy approaches, aiming for integrated planning and coherent management. Understanding how regionalization processes work to enhance legitimate and responsible governance leading to improved sustainability persists one of the main challenges to Marine Governance. Marine Governance involves processes of interaction between state actors, market parties, supranational organizations and civil society in a multi-level and multi-layered institutional setting. We argue that processes of integration and cooperation are core drivers to regionalize previous European – state based institutions. Accordingly, the main aim of this article is to provide a framework to unravel the challenges of integration and cooperation in Marine Governance. Particularly through processes of regionalization, i.e. when redefining territorial spaces and recomposing political spaces at the regional sea level, this framework is used to assess how integration and cooperation perform in EU marine governance. Specifically, four modes of regionalization in Marine Governance have been identified depending on the level of cooperation and integration, referred to as: territorial synchrony, territorial anarchy, sectoral anarchy and sectoral synchrony. While some developments towards more territorial synchrony for EU Marine Governance is observed, more cooperative and integrated efforts will be needed to eventually become successful in moving from sectoral anarchy to the desired territorial synergy expressed in EU marine regulation.