The influence of conservation policies on environmental governance by indigenous peoples is not well understood. Our goal is to understand the role of conservation policies in the on-going social, spatial and temporal reorganisation of common natural resources management by the Wayãpi and Teko in French Guiana. Using socio-economic and land use variables, we explain their territorial reorganisation. We show how the delimitation of protected areas encourages identity claims and resources re-appropriation, which play a determining role in territorial reorganisation. Finally, we focus on the emergence of a new form of environmental governance based on “multi-sited” land use system.