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This research is motivated by the compelling finding that the illicit cocaine trade is responsible for extensive patterns of deforestation in Central America. This pattern is most pronounced in the region's large protected areas. We wanted to know how cocaine trafficking affects conservation governance in Central America's protected areas, and whether deforestation is a result of impacts on governance. To answer this question, we interviewed conservation stakeholders from key institutions at various levels in three drug-trafficking hotspots: Peten, Guatemala, Northeastern Honduras, and the Osa Peninsula in Costa Rica. We found that, in order to establish and maintain drug transit operations, drug-trafficking organizations compete with and undermine conservation governance actors and institutions. Drug trafficking impacts conservation governance in three ways: 1) it undermines long standing conservation coalitions; 2) it fuels booms in extractive activities inside protected lands; and 3) it erodes the territorial control that conservation institutions exert, exploiting strict “fortress” conservation governance models. Participatory governance models that provide locals with strong expectations of land tenure and/or institutional support for local decision-making may offer resistance to the impacts on governance institutions that we documented.