Spondias mombin L. (Anacardiaceae) is an arboreal and allogamous fruit tree native from southern Mexico to southeastern Brazil, with great potential for economic exploitation. This study aimed to evaluate the structure and genomic diversity of yellow mombin accessions collected in nine locations in Brazil using Single Nucleotide Polymorphisms (SNP) markers. Significant genetic structure was observed in the discriminant analysis of principal components (DAPC) and dendrogram construction, in accordance with our hypotheses. The Mantel test identified a highly positive and significant correlation between geographic and genetic distances. The locations from the Amazon biome presented higher genetic diversity values when compared to those from the Atlantic Forest and Cerrado, which is expected considering the higher vulnerability of these biomes. However, although presenting greater genetic diversity, the Amazon biome showed positive inbreeding coefficients (F IS ) in three of the four locations, ranging from 0.0855 to 0.2421, indicating a potential risk of genetic erosion, possibly related to the increased degradation of this biome in recent decades. The results obtained contribute to the understanding of the distribution of genetic variation and conservation status of yellow mombin in Brazil. They could also be used as a subsidy for developing conservation strategies and the genetic improvement of this species.