The cajuzinho do cerrado (Anacardium humile St. Hill) is widely distributed species undergrowth in the Cerrado which is subject to the deleterious effects of fragmentation of this biome. In this work, we studied 333 genotypes of 14 people population preserved in the germplasm collection of UFG Regional Jataí on nine microsatellite loci, in order to analyze the diversity and population structure and test the causes of differentiation of populations. Anacardium humile A. St. Hil has a high genetic diversity in all populations with 185 alleles found, an average of 20.55 per locus. The populations showed an overall average of 85.3 alleles per population revealing a high information content associated with microsatellite markers. The expected average values of heterozygosity (He) and observed (Ho) loci were found to 0.876 and 0.656 respectively. The coefficient of inbreeding within the population ranged from -0.016 to 0.310 with an average of 0.169, indicating that allelic frequencies are not following proportion expected for the Hardy-Weinberg equilibrium. The analysis of the genetic structure of the dendrogram generated from the matrix of genetic distances allowed the formation of groups 7, showing the genetic diversity of genotypes. The genetic divergence between populations was relatively low (9.6%). The gene flow values found indicate that the metapopulation structure of A. humile St. Hill is not yet committed. The correlation between genetic distance matrix with and geographic distance matrix proved inefficient in the divergence found among populations.