Objective The ichthyofaunal diversity of the Great Basin is incompletely characterized, with the Wall Canyon Sucker Catostomus sp. being one potential species. The Wall Canyon Sucker is limited in distribution to the Wall Canyon drainage of Surprise Valley, Washoe County, Nevada, USA. It was first documented and collected by C. L. Hubbs and R. R. Miller in 1934, and no species description has been published to date. Nonetheless, the Wall Canyon Sucker has been treated as a species and has appeared in various contexts within and outside of the scientific literature as such. Methods We conducted phylogenetic analyses and the first population genetics study of this putative species using genome‐wide sampling obtained through restriction site‐associated DNA sequencing to assess the Wall Canyon Sucker's relationships and population genetic characteristics. Result We found the Wall Canyon Sucker to be sister to the Warner Sucker C. warnerensis with high support and a median divergence time of 2.12 million years. Population genetic analyses supported that the Wall Canyon Sucker is a single genetic population with a high degree of isolation. Principal components and admixture analyses did not indicate recent admixture of the Wall Canyon Sucker with the Warner Sucker. Substantial differences in allele frequencies between the Wall Canyon and Warner suckers were apparent (genetic differentiation index FST = 0.15–0.21). Nucleotide diversity in the Wall Canyon Sucker was the lowest of all observations, and Tajima's D was greater than zero (D = 1.96), indicating population contraction and a lack of rare alleles, congruent with the desiccation of Lake Surprise and the persistence of the fish in a very restricted recent range. We undertook species delimitation with publicly available mitochondrial gene sequence data and found that a species‐level designation of the Wall Canyon Sucker is appropriate in that framework as well. Conclusion The results of this study are consistent with recognition of the Wall Canyon Sucker as a species; however, it still requires a formal taxonomic description.