Pantosteus, a subgenus of Catostomus, includes the mountain sucker (Catostomus playthyrnchus), whose speculated older origins in the Miocene/Pliocene can provide insight into the ancient geographical events of western North America. We believe that major geologic events influencing the diversification of mountain suckers include the rise of the Colorado Plateau, the connections between the ancient Snake River system and the Lahontan system and subsequently the connection of the Snake River system to the Columbia Basin, dispersal of mountain suckers across the continental divide, as well as the Pleistocene Bonneville flood. If this is true, we should see evidence of geologic separation and timing through studying the phylogenetics of the mountain sucker. In order to clarify relationships of the mountain sucker with respect to other Pantosteus species, we examined cytochrome b (cyt b) sequences for 144 mountain suckers, 24 other Pantosteus species, and ten outgroup species. Phylogenetic relationships among haplotypes were constructed based on maximum likelihood and Bayesian criterion. In an effort to provide better resolution at some nodes, we also sequenced additional mitochondrial genes (ND1, ND2, ATPase, ND4L, ND4, ND5, ND6, and cyt b) for a subset of 44 individuals taken from the major clades obtained from the cyt b phylogentic analyses. Trees from this data set were also constructed under maximum likelihood and Bayesian criterion. All phylogenetic analysis revealed that mountain sucker are paraphyletic, with two major clades of mountain suckers separated by other members of the subgenus Pantosteus. One clade included two sub-clades, one from the upper Snake River drainage/northern Bonneville/Green River drainage Basins and the other from the southern Bonneville Basin. The other major clade included sub-clades from the Lahontan Basin, Columbia River Basin, and Upper Missouri River Basin. Molecular clock analysis revealed that Pantosteus likely split from Catostomus during the Miocene and that major speciation events within Pantosteus occurred during the Pliocene and Pleistocene. Genetic structuring and gene flow estimates for mountain sucker populations, with groupings based on major drainage basins, were calculated with AMOVA and Fst estimates in Arlequin and revealed that most of the genetic structuring was explained by variation among drainage basins with limited gene flow occurring between drainage basins. Based on this study, the role of the Colorado Plateau's geologic history in the evolution of the mountain sucker remains unclear. However, all other geologic events as discussed in this study seem to have played a significant role in the evolution of the mountain sucker.