The vast majority of the global biological diversity is hosted in tropical countries. At the same time, these are the most highly populated countries and suffer instability as a result of their particular socioeconomic and political circumstances. In these contexts, the debate surrounding the expansion of protected areas for biological conservation has been exhausted. It has been proved that the protectionist and colonialist ‘pristine’ and ‘people-free’ focuses of protected areas are inoperative. The biodiversity is found in the same territories that are shared by millions of inhabitants, and represents sources of food, medicine and income through raw materials and transformed products. Biodiversity has been used and transformed by thousands of ethnic groups and communities for millennia, generating a valuable heritage of traditional knowledge for its management. However, historically, the traditional disciplines of ecology and conservation science have ignored these contexts and knowledge. This disconnection has generated a considerable gap between the technical knowledge of conservation and the need to develop viable and effective management strategies. The science of conservation requires an evolution towards transdiscipline, within an integrative framework that can accommodate all of the voices and languages of the pertinent stakeholders. Implementation of top-down conservation strategies that only consider purely biological objectives is doomed to failure. Any effort of conservation planning must be constructed in a complete analysis of the local context, where the objectives of conservation must be aligned, as far as possible, with social and economic objectives that will allow landowners and local inhabitants to address their basic needs. I illustrate these issues through several case studies of conservation policies in Mexico related to protected areas management, endangered species management and community land co-management. Alternative solutions for conservation planning that incorporate bottom-up approaches, with plural representation, consensual agreements of collaboration and shared benefits through co-management are presented.