Closely-related unionid species often overlap in shell shape and can be difficult to accurately identify in the field. Ambiguity in identification can have serious impacts on conservation efforts and population surveys of endangered species. Truncilla donaciformis and T. truncata are sister species that overlap in their distributions and frequently co-occur in central North America. Because T. donaciformis is endangered in Canada and imperiled in some U.S. jurisdictions, co-occurrence with the morphologically-similar T. truncata means that misidentification could have serious impacts on status assessments and recovery efforts. The objectives of this study were: (1) to employ morphometric analyses in combination with DNA barcoding to quantify morphological differences between T. donaciformis and T. truncata and (2) to use these methods to confirm field identifications and identify problematic specimens. Truncilla specimens were photographed and visceral mass swabs taken from four rivers in southern Ontario. Positive identifications of all specimens were obtained through sequencing a fragment of COI mtDNA. Generated sequences were compared to published data from NCBI Genbank using BLAST. Traditional and geometric morphometric approaches were used to assign specimens to species. Assignments generated were compared to identifications based on mtDNA barcodes, with traditional and geometric morphometric analyses found to be 90.3% and 99.0% accurate in species identifications, respectively. This study confirmed the presence of T. donaciformis in Ontario’s Thames River, and revealed that all mussels collected for this study from the other three rivers were T. truncata. This study reinforces the utility of combining geometric morphometric analyses and DNA barcoding for identifying problematic unionid specimens.