As education shapes the thinking of the next generation of researchers, its conceptual framework, analytical tools and the way in which these interact with their natural surroundings, will significantly impact scientific studies, policies and decision making. The objective of this article is to analyze how graduate programs in Chile related to ecology and natural resource management are integrating socio-ecological aspects in their courses of conservation biology. Additionally, we present our perspectives about the processes, benefits and challenges that arise with participation in programs with interdisciplinary emphases. In Chile, we reviewed 22 graduate programs (nine doctoral and thirteen master's) related to themes of ecology and natural resource management and certified by the National Accreditation Commission as of October 2008. Of them, 64 % had a course in Conservation Biology. In spite of some integration of socio-economic aspects in the contents of these courses, the educational perspective of these continues to be within a utilitarian paradigm, which contrasts from broader approaches encompassed within environmental philosophy. We propose that it is necessary to change the teaching paradigm of conservation biology in Chile, such that it addresses social and ecological aspects that transcend utilitarian and instrumental values, incorporating the human being within ecosystems and the non-equilibrium ecosystem model. To integrate the socio-ecological perspective in conservation courses, we propose the inclusion of four educational components: (a) biocultural approach, (b) interdisciplinarity, (c) multi-directional communication and participation, and (d) field experiences and direct encounters with nature and the local communities. © Sociedad de Biología de Chile.