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Stenocereus eruca (Cactaceae), a prostrate cactus endemic to the Sonoran Desert, is thought to be highly clonal. We examined its clonal diversity and distribution: (1) at the population level, in four distinct populations along its distribution range; and (2) at a micro scale level, within a single population. Our objective was to evaluate the importance of sexual versus clonal recruitment through the use of RAPD markers. Contrary to previous field observations, clonal diversity was relatively high across the distribution range. This finding suggests that sexual recruitment is an important regeneration mechanism. The proportions of distinguishable genotypes (G/N = 0.83) and genotypic diversity (D = 0.987) were greater than in other clonal cacti, suggesting that clonal propagation is not the major regeneration mechanism. Autocorrelation analyses revealed a spatial genetic structure that may be the result of restricted gene flow (via pollen or seeds) and clonal propagation. A molecular variance analysis (AMOVA) indicated that most of the variation (66.3%) was found within and not across populations. Future studies on pollen and seed dispersal are needed to understand the role of the clonal habit in the mating system of S. eruca.