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Livelihoods of people living in many protected areas (PAs) around the world are in conflict with biodiversity conservation. In Mexico, the decrees of creation of biosphere reserves state that rural communities with the right to use buffer zones must avoid deforestation and their land uses must become sustainable, a task which is not easily accomplished. The objectives of this paper are: (a) to analyze the conflict between people's livelihoods and ecosystem protection in the PAs of the Sierra Madre de Chiapas (SMC), paying special attention to the rates and causes of deforestation and (b) to review policy options to ensure forest and ecosystem conservation in these PAs, including the existing payments for environmental services system and improvements thereof as well as options for sustainable land management. We found that the three largest PAs in the SMC are still largely forested, and deforestation rates have decreased since 2000. Cases of forest conversion are located in specific zones and are related to agrarian and political conflicts as well as growing economic inequality and population numbers. These problems could cause an increase in forest loss in the near future. Payments for environmental services and access to carbon markets are identified as options to ensure forest permanence but still face problems. Challenges for the future are to integrate these incentive mechanisms with sustainable land management and a stronger involvement of land holders in conservation.