This paper focuses on the management of protected areas in transboundary contexts and centres on the contemporary evolution of the border between Chile and Argentina in Northern Patagonia, which is a region that has witnessed the creation of numerous protected areas that are currently claimed by Mapuche organisations and communities as part of their customary territory. In response to these claims, both states have progressively integrated Mapuche communities into the management of protected areas through specific agreements. Many of these protected areas have also been included in a Transboundary Biosphere Reserve proposal for UNESCO. A new environmental governance model that includes the protection of indigenous peoples' rights is under construction not only along but also across the border between Chile and Argentina. Therefore, we discuss how participatory management could be viewed as a tool for redefining borders by linking environmental security in protected areas to human security in Mapuche communities. The article seeks to understand the role of environmental governance in shaping and/or overcoming political boundaries, and analyse how strategic mobilisations of the environment can advance the achievement of competing territorial projects led by different actors in different periods.