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In light of ongoing socio-ecological challenges facing the Arctic Ocean, the Ecosystem Approach (EA) has been increasingly proposed as a promising method to address and manage the effects of multiple stressors on Arctic marine ecosystems. Yet, the rights and roles of Arctic Indigenous peoples in implementing the EA in the marine Arctic remains underexplored. This article approaches this issue along two lines. It first provides a theoretical discussion on the rights and role of Indigenous peoples in the implementation of the EA as based on international law and relevant regional developments pertinent to the Arctic. The article then analyses the extent to which Indigenous peoples are currently involved in the practical implementation of the EA in managing marine biodiversity in the Arctic by exploring two case studies: the management of the shared polar bear population across the waters of Alaska-Chukotka, Baffin Bay and Kane Basin, and the Southern Beaufort Sea; and the management of biodiversity in the transboundary marine ecosystem of the North Water Polynya (Pikialasorsuaq).