We sequenced 556 bp of the mitochondrial ND5 gene to infer aspects of population structure and to test subspecific designations of argali sheep (Ovis ammon) in Mongolia. Analysis of molecular variance (AMOVA) revealed greater variation within than among putative subspecies and populations, suggesting high levels female-mediated gene flow. Compared with bighorn sheep (O. canadensis) in North America, substantially less differentiation in mitochondrial DNA was found among argali populations over 1200 km than was found among bighorn populations over 250 km. This result is consistent with differences in argali and bighorn life history traits. Argali run for long distances across open terrain in the presence of a threat rather than running up into steep escape terrain like bighorn sheep do. Our results suggest recognizing only one Evolutionary Significant Unit (subspecies) of argali in Mongolia, but they may support recognizing two Management Units, because two regions do exhibit slightly different haplotype frequencies at the ND5 gene of mtDNA.