Population genetics of wild, managed in situ and cultivated populations of Stenocereus pruinosus coexisting in Central Mexico were studied. We hypothesized that artificial selection decreases genetic diversity in managed populations and influences differentiation of populations depending on the amount of gene flow. Nine wild, managed in situ and cultivated populations (264 individual plants) were studied through isozyme analysis (10 loci). Genetic variation of S. pruinosus is the highest reported in columnar cacti species (e.g. HT=0.592). Genetic variation in cultivated populations (Ho=0.611, He=0.588) was slightly higher than in wild (Ho=0.556, He=0.583) and managed in situ populations (Ho=0.536, He=0.578), but differences were not significant. Most of the genetic variation occurred within populations, with low differentiation and high gene flow among all populations (FST=0.064, NmFST=3.659 and NmGST=3.803 in average) associated to bat pollination, seed dispersal by birds and transportation of vegetative propagules by people. Genetic distances were not correlated with geographic distances and in most cases are lower between similarly managed populations. Managed in situ and cultivated populations are important reservoirs of genetic diversity of this species to be considered in conservation programs. © 2008 Elsevier Ltd. All rights reserved.