Escontria chiotilla is a columnar cactus that grows in the arid and semiarid lands of Central Mexico and produces edible fruit with economic. In the wild, this plant species is distributed as part of thorn-scrub and tropical deciduous forests, but in the Tehuaca´n Valley also occurs in silvicultural managed in situ populations, in which people practise artificial selection enhancing phenotypes with larger fruits. The population genetics of wild and managed populations was studied to analyse the effects of management on genetic structure of E. chiotilla. A total of 150 individuals from six populations were studied, analysing 13 loci for eight enzymes by starch gel electrophoresis. The genetic variation in wild populations was significantly higher than in managed populations (H o = 0.079, H e = 0.134, H T = 0.370, and H o = 0.052, H e = 0.110, H T = 0.298, respectively), indicating that silvicultural management has caused a reduction of the genetic variation in populations. Most of the genetic variation in both wild and managed populations occurs within populations (D ST = 0.027 in the wild and 0.018 in managed populations). The genetic distance coefficients were slightly different for silvicultural managed populations than in wild ones, illustrating an incipient effect of management on the genetic structure of populations. However, values of Nm GST = 3.845 and Nm FST = 3.848 indicate that a high gene flow counteracts the effects of human selection on the differentiation of populations.