The Caesalpinia hintonii complex is formed by five endemic species (C. hintonii, C. laxa, C. macvaughii, C. melanadenia and C. epifanioi) occurring in central Mexico. This species complex is under incipient genetic divergence as by-product of local adaptations in reproductive and morphological traits to different habitats. We estimate the genetic variation and structure of populations of this species complex to assess the extent of genetic differentiation among populations and related species along its geographic distribution. Estimations of genetic diversity and structure were done based on ten enzymes and 18 loci. Mean number of alleles per locus ranged from 1.5 to 1.9. Polymorphic loci ranged from 42.1 to 68.4. Observed (Ho: range 0.1910.275) and expected (He: range 0.2050.317) heterozygosities in this complex were higher compared with other endemic and legume species. Neis genetic diversity estimates showed that most genetic variation was found within (HS = 0.325) rather than among populations (DST = 0.085). Populations of the species C. hintonii showed a considerable genetic differentiation (FST = 0.207). The results of genetic diversity and structure within and among populations are in accord with the great morphological differentiation described for this species complex.