Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 published genomes. Phylogenetic comparisons of the mtDNA and nucDNA genomes show extensive phylogenetic discordance suggesting that the evolution of the two types of genetic material is not identical. The SNPs for each strain analyzed, the raw files for phylogenetic trees and the list of SNPs designated as unlinked and allele frequencies used as input for STRUCTURE analysis were made available.