Discerning the biogeography and historical ranges of organisms is important to understanding the processes causing population divergence and speciation. Mountainous regions in North America have contributed to widespread divergence within animals and plants as species become geographically isolated and diverge. Here, we investigate patterns of divergence for six species of walnut-infesting flies in the Rhagoletis suavis species group (Diptera: Tephritidae) in the United States and Mexico based on sequence analysis of mitochondrial DNA (mtDNA) encoded Cytochrome Oxidase I and II genes (COI and COII). We resolved the relationship of the newly described species, Rhagoletis ramosae, found in the highlands of Mexico, within the R. suavis species group to test alternate hypotheses of migration and divergence. Bayesian phylogenetic analysis supported a clade in which R. ramosae was most closely related to Rhagoletis zoqui/Rhagoletis completa, found in eastern Mexico. This implies that the Sierra Madre Oriental and not the Sierra Madre Occidental have been a major conduit of migration, isolation, and speciation for walnut flies between Mexico and the United States. Comparisons of mtDNA divergence for R. suavis group flies with the Rhagoletis pomonella and Rhagoletis cingulata species groups suggested that despite current similarities in geographic distributions, these taxa do not share a common biogeographic history, diverging in different regions at different times in the past. Patterns displayed by Rhagoletis flies can be compared to patterns seen in other organisms through the Southwestern and Eastern United States, and Mexico to develop a fuller understanding of the biogeography of these regions of North America.