Traditionally, methods for phylogenetic and phylogeographic inference have relied heavily on morphological data. Molecular data can provide an independent assessment of patterns and are particularly desirable when morphology may be under natural selection. Herein we present a phylogeographic analysis of the highly polytypic butterfly, Speyeria callippe. Samples were drawn from 71 populations across western North America. Phylogeographic trends are inferred from analysis of the gene Cytochrome oxidase subunit I ( CoI ). Patterns of mtDNA diversity imply historical panmixia and Mid-to-late Pliocene divergence from other Speyeria approximately xx mya. Diversification within the species appears to have occurred primarily during the Pleistocene. The data partially support a hypothesis of multiple waves of diversification following the climatic fluctuations of glacial and interglacial periods. Speyeria callippe was found to be paraphyletic containing both Speyeria egleis and Speyeria edwardsii. The genetic variation observed within S. callippe was highly structured reflecting local geography. However, this did not extend to larger scales as subspecies and major color pattern groups were not recovered as monophyletic, consistent with the large amount of overlapping morphological variation. Overall, intraspecies differentiation in morphology and mtDNA observed here indicate S. callippe is a young species complex with potentially adaptive color pattern variation that is in a relatively early stage of sorting into geographically separate entities.