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Agave cupreata Trel. & Berger is an endemic plant naturally distributed in the Balsas Depression, a semiarid region in the states of Guerrero and Michoacan in Southwestern Mexico. Their populations are heavily decimated because mature individuals just before their single life flowering period are harvested to produce mescal, an alcoholic beverage. The genetic variation among and within 12 natural populations was examined for nine isozyme loci. Results indicate high average proportion of polymorphic loci (93 %) and expected heterozygosity (H-c = 0.467), with an excess of observed heterozygotes in relation to Hardy-Weinberg expectations (H-D = 0.521, F-IS = -0.1179). These results represent the largest heterozygosity reported for Agave species endemic to Mexico. There is also a statistically significant genetic differentiation among populations (F-ST = 0.042). An UPGMA dendrogram reveals the absence of a geographic pattern, as confirmed by a Mantel test (r = -0.110, P = 0.769), which did not show significant isolation by distance. Estimated minimum viable effective population size was very large (N-c = 16,165), larger than in any other known natural population. To protect the natural genetic variation, it is suggested to design and manage A. cupreata natural populations as forest genetic resource conservation units (FGRCUs) using realistic and modest N-e sizes, perhaps between 500 and 5000 plants, ideally with intermediate plantations that could serve as pollinator corridors. Commercial plantations and ex situ FGRCUs need to be established to gradually develop a sustainable management, perhaps at higher altitudes than current locations, as a management measure for adaptation to the climatic change.