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In Mexico and in other parts of Latin America, a large overlap can be observed between indigenous territories and regions of high biological value. In this paper, we ask if the same overlap can be observed in the state of Jalisco, in western Mexico. To answer this question, we start with a succinct analysis of the two main indigenous regions in rural Jalisco: the Huichol Sierra in the northern part of the state and the Sierra of Manantlán, in the southern part. Then, we extend our analysis to the state in its entirety in order to measure the overlap between indigenous territories that have been "desindianized" and regions of high biological value. This is done by comparing the municipalities that contain agrarian centers designated as "indigenous communities" and the municipalities that areas officially recognized for their ecological importance. A high correlation between these two variables is observed, leading to the question "why". A series of hypotheses is developed and these are contrasted with empirical evidence through a case study of the ejido of Ayotitlán, in the Sierra of Manantlán. Although different forms of environmental degradation can be observed in Ayotitlán, it continues to be one of the best conserved territories in the state of Jalisco, with high levels of biodiversity. This is due, not only to its isolation, but also to the way in which the indigenous inhabitants have interacted with the environment and because of their activism in defense of their territory and natural resources. [ABSTRACT FROM AUTHOR]