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Agave potatorum is a wild endemic species of Mexico. Its stems are used for mescal production, which cancels sexual reproduction. Agaves extraction from forests decreases their reproductive success and demographic performance. We evaluated patterns of genetic diversity and structure of wild populations under and without extraction in order to identify effects of its use and actions required for conserving genetic variation. This study was conducted with seven SSR markers in 12 populations representing the entire distribution area of the species. Standard parameters of genetic diversity, differentiation, structure and genetic similarity of populations were calculated and analyzed. The populations studied showed intermediate to high genetic diversity (H (e) = 0.36-0.64), compared with other Agave species so far studied. The wild category was the most diverse (H (T) = 0.87), but without significant differences with respect to populations under extraction (H (T) = 0.72), and two germplasm banks sampled (H (T) = 0.69). High structure among populations (I broken vertical bar (PR) = 0.38) and inbreeding levels (F (IS) = 0.26, F (IT) = 0.55) were identified; a 3 % of genetic diversity being distributed among management status where germplasm banks represent a genetic pool with incipient divergence from the other categories. Bayesian analysis indicated two genetic groups. Our study suggests slight effects of management on genetic diversity of A. potatorum, apparently related to alterations of reproductive biology and pollination patterns.