Microsatellite markers were used to obtain direct and indirect estimates of gene flow in populations of Polaskia chichipe under different management regimes, in order to understand the genetic consequences of gene flow in the evolutionary process of domestication. P. chichipe is a columnar cactus endemic to the Tehuacan Valley, Central Mexico, and has come under domestication for its edible fruit. Morphological, phenological, physiological, and reproductive differences, apparently attributable to artificial selection, exist between wild and managed populations, which grow sympatrically. However, strong gene flow may counteract the effects of this selection. In this study, we used paternity analysis to demonstrate that although most of the pollinations occur among individuals within the same population at distances < 40 m, pollen flow from other populations is considerable (27 ± 5%). Heterogeneity in pollen clouds sampled by mother plants (FST = 0.12) indicated nonrandom mating, which is probably due to temporal heterogeneity in pollen movement. Spatial structure on local and regional scales is consistent with an isolation-by-distance model. The similarity of indirect, direct and demographic estimates of neighbourhood size (74–250 individuals) suggests that this genetic structure is representative of an equilibrium state. These results suggest that traditional management practices have conserved the genetic resources of this species in situ, but also that gene flow is counteracting the effect of domestication to some degree. We discuss our results in the general context of genetic exchange between cultivated and wild populations during the domestication process.