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Abstract This paper describes the utility and application of a methodology for monitoring, assessing and managing Large Marine Ecosystems (LMEs) that has been applied in projects receiving financial assistance from the Global Environment Facility (GEF) over the last two decades. In particular, the paper focuses on practical integration of the methodology, known as the Large Marine Ecosystem approach (or simply LME approach), into diagnostic and strategic planning documents required by the GEF on collaborative projects to restore and manage LMEs. Examples from several successful LME projects are provided to highlight how this methodology has been adapted and integrated by countries into LME strategic programs and project operation. This paper demonstrates that the LME approach not only provides a useful framework for holistic, ecosystem-based assessment and management of transboundary marine ecosystems but also complements GEF guidance and requirements for monitoring and evaluation on projects in its International Waters focal area.