Abstract Political strategies undertaken by nation-states to conserve biodiversity, particularly through the creation of protected areas (PAs), have had deleterious impacts on many local and indigenous groups worldwide. Increasing recognition of these impacts has led to calls for more democratic conservation strategies and indigenous rights recognition in PAs. Addressing this legacy requires an understanding of the complexity and diversity of past experiences as well as an appreciation of the factors that might support the establishment of more democratic arrangements within contemporary PA contexts. Focusing on the experience of Chile, where twenty-nine percent of state-designated PAs are established on indigenous territories, separate lines of inquiry are explored in each of two manuscripts that comprise the core of this thesis. The first examines the history of Chilean state engagement with PAs in relation to an analysis of the state’s evolving rationalities for the creation and expansion of PAs on and into indigenous territories and the resulting impact of state-led strategies of territorialization on indigenous peoples. The second investigates recent and emerging relations between the State and indigenous peoples as outcomes of particular instances of resistance, accommodation and negotiation in PA contexts. Particular attention is given to the factors that support the meaningful participation of indigenous peoples in the governance of PAs. The research is written from my vantage point as a Chilean geographer with a professional background in PA policy and is based on literature and document analysis, as well as interviews with representatives from Chilean state government agencies, non-governmental organizations, academic institutions and indigenous organizations.