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The black bear Ursus americanus is one of the largest terrestrial carnivores that has a wide distribution in northeastern Mexico, the only country in which black bears are listed as endangered. We used 10 nuclear microsatellite loci to evaluate black bear genetic variability in 6 disjointed populations from northeastern Mexico. Non-invasive genetic techniques were applied to fecal and hair samples. Using a panel of 10 polymorphic microsatellites we identified 64 individuals. Black bears showed low to moderate levels of genetic diversity in all sampled populations (mean +/- SD expected heterozygosity, H-e = 0.63 +/- 0.628). Pairwise comparisons between all 6 populations (phi(ST) = 0.315, p < 0.05) detected significant genetic differentiation between the western Coahuila and the northeastern Nuevo Leon regions, suggesting that black bears have low levels of gene flow between these 2 regions. Microsatellites revealed significant structure within the complex of disjoint areas in the region. The inbreeding coefficient was also significant (phi(IS) = 0.143). The largest proportion of genetic variation (82.7%) was found between individuals within populations. Distance and anthropogenic activities may serve to limit gene exchange among populations which form at least 3 distinct genetic clusters; these may respond differently to environmental changes and should be considered distinct management units.