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The application of ecosystem-based management (EBM) in marine environments has been widely supported by scientists, managers, and policy makers, yet implementation of this approach is difficult for various scientific, political, and social reasons. A key, but often overlooked, challenge is how to account for multiple and varied human activities and ecosystem services and incorporate ecosystem-level thinking into EBM planning. We developed methods to systematically identify the natural and human components of a specific ecosystem and to qualitatively evaluate the strength of their interactions. Using the Gulf of Maine marine ecosystem as a case study, we show how these methods may be applied, in order to identify and prioritize the most important components to be included in an EBM plan - particularly the human activities that are the strongest drivers of ecosystem change and the ecosystem services most threatened by cumulative and indirect effects of these activities. [ABSTRACT FROM AUTHOR]