Polaskia chende is a columnar cactus endemic to central Mexico, where it is managed via silviculture due to its edible fruits. We aimed to analyse the consequences of management on population genetics and compared information from different markers to analyse ecological and evolutionary aspects of incipient domestication and genetic resources conservation. Eight populations were evaluated using seven microsatellite loci and 15 allozyme loci. SSR identified higher genetic diversity (A = 5.6, p = 98.2, HE = 0.651) than allozymes (Ar = 2.6, p = 93.3, HE = 0.479). Both marker types identified that HO and HE were higher in wild populations (SSR: HO = 0.730; HE = 0.677; allozymes: HO = 0.432; HE = 0.481) than in the managed ones (SSR: HO = 0.652; HE = 0.616; allozymes: HO = 0.417; HE = 0.474), but differences were significant only analysed by SSR. SSR identified 3 % of genetic structure between wild and managed populations and 10 % among populations (ϕPR = 0.099), a much lower estimate than with allozymes (ϕPR = 0.208). The results suggest that management has had only slight consequences on the population genetics of P. chende. Artificial selection operates at low intensity and life history traits of the species, particularly the self-incompatible breeding system, pollination by bees and seed dispersion by birds, bats and humans favour high genetic diversity and gene flow. SSR detect finer genetic variation than allozymes, but both marker types provide similar patterns of information useful for analysing population genetics.