Similar morphology and confused historical taxonomy of Hybognathus hankinsoni (brassy minnow) and Hybognathus placitus (plains minnow) have made determination of their historic distributions and conservation status unclear in eastern Colorado basins. We developed logistic regression models from morphometric measurements to predict species identity of Hybognathus collections from Colorado and adjacent counties (n = 1154 specimens in 134 lots). A model based on orbit diameter, standard length, and eye position correctly predicted 98% of the specimens examined and 100% of the museum lots. Hybognathus hankinsoni have larger eyes centered on a horizontal line through the tip of the snout, whereas H. placitus have smaller eyes centered above the tip of the snout. The two species were historically sympatric in the Platte, Republican, and Smoky Hill River basins, whereas H. placitus was allopatric in the Arkansas River basin. The taxonomic characters defined here will allow accurate identification of future collections to determine the status of these native fishes.