Abstract: Dipteryx alata Vogel (Leguminosae) is a native Neotropical tree with a wide distribution in the Brazilian Cerrado that is commonly known as the baru tree. The genetic diversity of 150 D. alata progeny from a germplasm collection was characterized using nine microsatellite markers. Genetic diversity analysis detected 50 alleles ranging from 2 to 14 alleles per locus. The genetic differentiation among populations (ϑp = 0.097) suggests moderate genetic structuring and high genetic differentiation among progenies (ϑs = 0.169). The intrapopulation index (f = 0.122) indicates the presence of low endogamy. The effective population size (Ne = 96) shows that the germplasm collection has sufficient representativeness for use as a base population for breeding programmes. These results are useful for the exploitation of the genetic resources of D. alata for future conservation efforts and breeding programmes.