Polaskia chichipe is a columnar cactus under artificial selection in central Mexico because of its edible fruits. Our study explored the effect of human manipulation on levels and distribution of genetic variation in wild, silviculturally managed and cultivated sympatric populations. Total genetic variation, estimated in nine populations with five microsatellite loci, was HT = 0.658 ± 0.026 SE, which was mainly distributed within populations (HS = 0.646) with low differentiation among them (FST = 0.015). Fixation index (FIS) in all populations was positive, indicating a deficit of heterozygous individuals with respect to Hardy–Weinberg expectations. When populations were pooled by management type, the highest expected heterozygosity (HE = 0.631 ± 0.031 SE) and the lowest fixation index (FIS = 0.07) were observed in wild populations, followed by cultivated populations (HE = 0.56 ± 0.03 SE, FIS = 0.14), whereas the lowest variation was found in silviculturally managed populations (HE = 0.51 ± 0.05 SE, FIS = 0.17). Low differentiation among populations under different management types (FST 0.005, P < 0.04) was observed. A pattern of migration among neighbouring populations, suggested from isolation by distance (r2 = 0.314, P < 0.01), may have contributed to homogenizing populations and counteracting the effects of artificial selection. P. chichipe, used and managed for at least 700 generations, shows morphological differentiation, changes in breeding system and seed germination patterns associated with human management, with only slight genetic differences detected by neutral markers.