Wabash Pigtoe, Fusconaia flava, and the related Round Pigtoe, Pleurobema sintoxia, are freshwater mussels (Bivalvia: Unionidae: Pleurobemini) native to the Great Lakes region of North America. Fusconaia flava is considered widespread and relatively common while P. sintoxia is considered an imperiled species. These species are similar in shell shape and coloration and have confounded many freshwater malacologists, resulting in frequent misidentifications. We sought to determine if morphometric analyses could be used to reliably distinguish between these species. Two hundred and forty-six specimens were collected from rivers in Michigan and Ontario. For each specimen, a preliminary identification was made, shell measurements and foot color (orange or white) were documented, and photos of the left shell valve were taken. A genetic sample was taken from 133 specimens for cytochrome c oxidase subunit 1 (COI) barcoding. COI sequences were used for species identification by comparing to sequences on GenBank. Twenty-one digitized landmarks along the outline of the left valve were analyzed and compared to the results of the DNA barcoding. Landmark data correctly assigned 99.2% of specimens to their DNA-confirmed species identity, compared to 82.0% accuracy of field identifications and 77.0% accuracy for foot color. The creation of a DNA-confirmed morphometric database will aid freshwater malacologists across the Great Lakes region in differentiating between these species.