Phylogeography and biogeography have been integral to our understanding of evolution and the speciation process. In addition, understanding how populations are related to one another both spatially and temporally has informed areas of research and policy such as conservation. The Bell's Vireo is a species of North American bird that inhabits the riparian systems of the southwestern and central portions of the United States, with large portions of its range located in both the Sonoran and Chihuahuan deserts of northern Mexico. The Bell's Vireo complex of four subspecies is of particular interest in conservation because of the endangered status of the western-most subspecies, the Least Bell's Vireo. The decline in the Bell's Vireo population, most notably in the Least Bell's Vireo, is attributed to many anthropogenic activities including development along riparian systems and cattle grazing. The increase in habitat fragmentation has led to an increased effectiveness of the brood parasite, the Brown-headed Cowbird, further decreasing population sizes. Subspecies descriptions are currently only based on qualitative description and therefore may not adequately represent evolutionary history. Thus, the objective of this study is to examine broad scale phylogeographic patterns in Bell's Vireo and evaluate the taxonomic distinctiveness of the endangered Least Bell's Vireo. Evolutionary relationships within the complex were reconstructed with mitochondrial ND2 and nuclear SNP data. I sequenced ND2 for 86 individuals from throughout the breeding range of the Bell's Vireo, and genotyped 48 individuals for genome-wide SNPs. Analyses of both datasets identified two major clades within the Bell's Vireo. The two clades follow an east/west divisional trend with a division at the Cochise-filter barrier along the Arizona and New Mexico border. The east and west clades are approximately 3% divergent in their mitochondrial sequence data. Using a Bayesian method (BEAST) and an ND2 divergence rate of 0.0115 per lineage per million years, I estimate the two clades diverged from each other 1.11 - 2.04 million years ago. The four subspecies are not diagnosable by their ND2 sequences, but all the Least Bell's Vireo samples formed a well-supported clade in the SNP dataset. Niche modeling, molecular dating, and comparative phylogeography suggest speciation resulting from allopatric refugia in the Sonoran and Chihuahuan deserts during glacial maximum. The 3% molecular divergence in mtDNA and concordance with the nuclear data argues for species recognition of the eastern and western forms, and the monophyly of Least Bell's Vireo in the SNP dataset supports maintaining its subspecies status.