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Magnolia tamaulipana is an endangered endemic tree found only in the El Cielo Biosphere Reserve in Tamaulipas, Mexico, historically subjected to anthropogenic disturbance. In this study, we assess the genetic diversity and structure of M. tamaulipana in the eight populations known to date. We used microsatellites to estimate the allelic diversity of 240 individuals and examined how this diversity is distributed among and within populations. We show that there is moderate genetic variation in its surviving populations (expected heterozygosity [ H E] ranged from 0.38 to 0.54) but low connection by gene flow (coefficient of differentiation [ F S T ] = 0.32). The four genetic groups detected (K = 4) were not isolated by distance. We suggest the existence of historical population reductions on the basis of the low diversity relative to other Magnolia species with similar distributions, the history of anthropogenic disturbances in the biosphere reserve, detected bottlenecks, and selective pressures in different locations. Recent bottleneck events due to environmental and landscape modifications probably led to increased genetic differentiation in M. tamaulipana. [ABSTRACT FROM AUTHOR]