Sigmodon hispidus, the hispid cotton rat, has a wide geographic distribution and has been the focus of numerous ecological studies; however, patterns of genetic divergence within this species remain largely unknown. Amplified fragment length polymorphism (AFLP) and mitochondrial cytochrome-b DNA sequence analyses were employed to document patterns of nuclear and mitochondrial DNA (mtDNA) divergence within this species. AFLP analysis of specimens from Georgia, Louisiana, Texas, Oklahoma, Kansas, and Arizona demonstrated that the previously recognized genetic discontinuity dividing S. hispidus into eastern and western mtDNA lineages also was evident in the nuclear genome. The contact zone between these 2 lineages was located in eastern Texas and hybridization was confirmed. The width of the hybrid zone was found to be 3 orders of magnitude greater than the estimated dispersal distance. This, in combination with an absence of linkage disequilibrium within the hybrid zone and its unimodality, suggests that selection is not a strong factor in the maintenance of the hybrid zone.