Anacardium humile Saint Hilaire is a tropical shrub native to the Cerradobiome. It's a fruit-bearing plant having biological, medical, and social value. Knowing how natural populations' genetic variability is arranged enables for the development of conservation and sustainable use plans for the species and its environment. Interest in genetic studies of natural populations that combine evolutionary biology and ecology has increased in recent years. This work aims to assess how natural populations of Anacardium humile, an important tropical shrub species native to the Cerrado biome, are genetically structured. Based on investigations of 242 adult plants, six microsatellite loci previously identified from Anacardium occidentale were utilised to evaluate the regional genetic organisation and genetic diversity of eight natural Anacardium humile populations. These communities have a high level of genetic variety (expected heterozygozygosity He = 0.710), according to the findings. With a mean of 0.142 (p = 0.001), the endogamy coefficient was positive and significant for most populations. Although the genetic divergence between groups was small (\(\theta\) = 0.075 and GST = 0.066), it was significant (p = 0.0001). The results show that genetic conservation measures for A. humile populations should be undertaken in order to keep this species alive.