The endangered Mexican long-nosed bat (Leptonycteris nivalis) is a migratory nectar-feeder that occurs in high-elevation, semi-arid, pine-oak woodlands and Chihuahuan Desert of central and northern Mexico as well as two localities within the southwestern United States. Little is known about migratory movements and population structure of this species. The primary objectives of this study were to measure variation and patterns of subdivision in maternally-inherited mtDNA, particularly addressing the hypothesis of female philopatry, and to compare this with the bi-parentally inherited AFLP (Amplified Fragment Length Polymorphism) data. A second objective was to infer historical demographics based on patterns of sequence variation. Genetic analysis of mitochondrial DNA (control region) and nuclear DNA (AFLP) revealed an absence of genetic structuring within L. nivalis. Nucleotide (π = 0.013) and haplotype (h = 0.810) diversity values for genetic data were comparable to other species of migratory bats and were moderately high for a species believed to have undergone a recent drastic decline in population size. Some patterns of mtDNA sequence variation (Fu’s FS and a network analysis) along with a lack of structure in the analysis of AFLP loci suggest a historic population expansion, but other analyses (Tajima’s D, Ramos-Onsins and Rozas’ R2, and a mismatch analysis) cannot reject stasis. It is concluded that individuals of L. nivalis form a panmictic population over a large geographic area. In addition, the geographic distribution of mtDNA control region haplotypes does not support the hypothesis of female philopatry.