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The overall aim of the Marine Strategy Framework Directive (MSFD) is to achieve or maintain Good Environmental Status (GES) within the marine environment. Turkey is in the process of using/developing an Ecosystems-Based Management approach for governance of its marine waters, based on the European Union (EU) Marine Strategy Framework Directive. The legislative history, conceptual approach, structure and content of the Directive, as well as some of its unique regulatory features are discussed here. The implementation of the MSFD represents a demanding task in the integrative assessment of marine ecosystems. Here we describe the implementation process, and we discuss the institutional framework and the main difficulties and challenges encountered so far, with emphasis on the Turkey context. This paper will provide a review of the existing institutional and legislative structure in Turkey relevant to the future implementation of the MSFD. Over the years Turkey has developed a robust body of Environment Law in general and a complicated institutional structure. One of the key priority elements for a successful implementation of the MSFD is the establishment of an effective framework for coordination and cooperation among national, regional and local authorities.