To investigate the genetic diversity and structure of Jatropha curcas L. oilseed plant, in this study, native populations from Chiapas, Mexico, were evaluated, using microsatellite DNA markers. A total of 93 representative samples were selected from seven sites in two regions in the state of Chiapas grouped by geographical proximity, where leaf samples were collected to isolate the genomic DNA. Individual polymerase chain reactions were carried out with ten pairs of specific oligonucleotides for the microsatellites of J. curcas, separating the products of amplification by acrylamide electrophoresis. Twenty-seven fragments were detected (77% polymorphic) with which heterozygous individuals were distinguished. The most informative microsatellite was Jcps20 (nine alleles, polymorphic index content 0.354). The average polymorphism per population was 58%. The Hardy–Weinberg tests revealed a reproductive pattern of non-random mating. The diversity descriptors and the analysis of molecular variance revealed that the populations were structured and moderately differentiated (F
ST 0.087) and that this differentiation was not due to isolation by distance, as the Mantel test was not significant (P= 0.137), but rather due to allopatry. Bayesian analysis revealed that the accessions belonged to only four genetic groups and confirmed the differentiation between the regions. Because some loci were in Hardy–Weinberg disequilibrium, it is proposed that differentiation is due to the clonal reproduction of J. curcas practised by farmers in Chiapas, along with the anthropogenic dispersion at regional levels. The results of this study reveal that J. curcas in Chiapas has genetic diversity that is greater than that reported in other parts of the world, which represents a potential germplasm pool for the selection of genotypes.