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Natural recolonization by large carnivores has rarely been documented. American black bears (Ursus americanus) recently (1988-present) recolonized portions of their former range in western Texas. We used mtDNA sequence data (n = 144 bears) from 7 populations of southwestern black bears in New Mexico, Texas, and northern Mexico to test predictions regarding metapopulation structure of the species in this region and the source of recolonization in western Texas. Six variable nucleotides were detected, resulting in 5 mtDNA haplotypes. Although within-site diversity of haplotypes (h) and nucleotides (pi) was low, a high degree of genetic partitioning among sites was detected (Phi(ST) = 0.6301). Analyses pinpointed northern Mexico as the source of black bears for western Texas. Female-mediated gene flow is proceeding slowly in this system (N(f)m = 0.4961 individuals/generation), but its occurrence was inferred via field observations. Nested clade analyses indicated that populations of bears in the Mexico-Texas region (area that encompasses mountain ranges within Nuevo Leon and Coahuila, Mexico, northward to smaller ranges located in the Trans-Pecos region of western Texas) were connected via restricted gene flow due to isolation by distance. Long-distance colonization is the likely cause of extant geographical associations between New Mexican and Mexico-Texas populations. The naturally fragmented, xeric environment of the Chihuahuan Desert impedes colonization, but is not a complete barrier to this process. Conservation initiatives concerning recolonization by black bears within the Mexico-Texas mainland-island metapopulation should focus on preventing human-bear interactions and maintaining corridors for dispersal between the mainland populations in Mexico and the island populations in western Texas.