Resumo. The loss of diversity in tropical regions has been focus on several governmental and non-governmental discussions, focusing mainly on the fragmentation and destruction of natural ecosystems. However, decisions about the conservation of genetic resources must be guided by population genetic parameters, especially for species with economic interests that are subject to greater human interference. This study aimed to define and evaluate genetic parameters for the conservation of populations of Hymenaea courbaril in southwestern Amazon. This species is one of the most valuable and intensively exploited wood species in the Brazilian Amazon. We studied three forest areas prepared for logging in the background of sustainable management. It was calculated with eight microsatellite loci, genetic diversity, intra-population conservation estimators and genetic divergence among populations. Genetic diversity and fixation index were higher in the low density populations (< 0.08 ind.ha -1 ). The most density population (0.25 ind.ha -1 ) showed the lowest genetic diversity and no inbreeding. The Minimum Viable Area for species conservation was consistent with the reality of the studied areas, with a proviso for one of the populations where there is a need for a much larger area than the other to conserve populations. The genetic divergence was high ( G’ ST = 0.344) and the populations were considered Independent Management Units.