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Agave cupreata and Agave potatorum are semelparous species distributed on dry tropical forests in south Mexico. Extraction of reproductive individuals for spirits production has caused a decline of wild populations and has raised concerns about their long-term conservation. We assess the degree of genetic erosion of exploited populations and provide population genetics baseline data for developing sustainable use strategies of these species. ISSRs (Inter Simple Sequence Repeats, dominant nuclear markers associated to microsatellites) were used to analyze five populations of each species throughout their distribution range. We found high levels of variation (P > 80%; H > 0.30) and moderate to high differentiation (A. potatorum theta = 0.120; A. cupreata theta = 0.172). Isolation by distance was significant in A. cupreata. Our data indicate that these species are not genetically eroded in general, and that they retain their historical patterns of diversity inside populations. Three genetically distinct populations are identified where conservation efforts should be a priority. Our results are discussed in relation to the in situ reinforcement of populations based on seeds propagation, in contrast to micropropagation practices that may threaten the genetic diversity of the species studied considering previous reports on genetic bottlenecks and inbreeding depression in Agave. (C) 2012 Elsevier Ltd. All rights reserved.