The summer tanager Piranga rubra is a Neotropical migrant that has experienced noted declines in the southwestern United States caused by extensive habitat loss of native riparian woodlands. This species is composed of two morphologically and behaviorally distinct taxa that traditionally have been recognized as subspecies, each occupying unique habitats in the southern part of North America. Genetic analyses of intraspecific variation are important in studies of threatened or endangered species because they can indicate whether smaller management units exist below the species level and they also provide estimates of within population variability. Using a mitochondrial DNA marker, the intraspecific genetic variation of this species is explored to determine whether the morphologically and behaviorally distinct subspecies are also genetically unique. By using traditional phylogenetic methods and building haplotype networks, results from this study indicate that the subspecies represent two phylogenetic species and should be managed as separate units. In addition, the level of gene flow among geographically isolated populations of the western subspecies is explored using Nested Clade Phylogeographic Analysis and population genetic tests. These analyses show that populations are genetically diverse and that haplotypes are shared across populations. Newly colonized populations are as diverse as older populations. This suggests that as habitat degrades in traditional breeding areas of the summer tanager, if suitable habitat elsewhere becomes available for new populations, these new colonies should be genetically diverse.