Each year, the etiologic agents, Coccidioides immitis and C. posadasii, cause Valley Fever in tens of thousands of individuals. While it widely accepted that this fungal disease is endemic to arid locations, such as the southwestern United States, the recent discovery of endemic clusters in Washington state suggests an expansion of the geographic range. Here, we present a whole genome analysis of 86 genomes, where 68 are unique to this study. The incorporation of Bayesian phylogenetics resulted in the identification of phylogeographic structure of both species, and calibrations on the root node reveal that C. posadasii is the more ancient of the two species. Taken together, we propose that C. posadasii originated near the Arizona-Mexico border, and we suggest a subsequent dispersal mechanism and route of spread.