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Stenocereus eruca and Stenocereus gummosus are two closely related columnar cacti of the Sonoran Desert that are thought to be highly clonal. In addition, it has been suggested that S. eruca has recently been derived from an S. gummosus-like ancestor. We used allozymes analysis to test these hypotheses and to describe levels of genotypic diversity in populations of both taxa. Allelic composition in S. eruca was a subset of the composition found in S. gummosus, while polymorphism and expected heterozygosity were greater in S. gummosus, supporting the hypothesis that S. eruca is a recently derived species. The proportion of unique genotypes (G/N) and genotype diversity (D) varied from 0.42 to 0.68 and from 0.78 to 0.98, respectively, among populations of S. eruca and from 0.64 to 0.96 and from 0.96 to 1.00, respectively, among populations of S. gummosus. The evidence on clonal diversity indicates that both species combine clonal growth and sexual recruitment as mechanisms of regeneration and that S. eruca seems to rely more on clonal propagation than does S. gummosus. We hypothesize that the procumbent growth habit of S. eruca in the plains of Magdalena may have evolved in response to aeolian dune formation during the Pleistocene.