Pyganodon grandis and P. lacustris, widespread and common species in North America, are known to co-occur across parts of their distributions. These mussels are genetically distinguishable with a sequence divergence between 9% and 13% for the mitochondrial (mt) DNA barcoding region, cytochrome c oxidase subunit I (COI), which is well beyond thresholds for distinct species. The objectives of this study were to (1) confirm the presence of two genetically distinct species (P. grandis and P. lacustris) in Font Lake and Lake Geneserath on Beaver Island in northern Lake Michigan, (2) identify hybrids using mitogenotype mismatch and (3) compare species and populations morphometrically. Of the 212 specimens sequenced, 146 (68.9%) were found to be heteroplasmic, with successful amplifications of both maternally (F-type, from mantle tissue) and paternally (M-type, from gonad tissue) inherited mt DNA sequences. Mismatches in species identity of the F- and M-type COI sequences were found in 22 specimens (15.1% of heteroplasmic specimens), with these being considered putative hybrids. Geometric morphometric analyses of shell shape reliably differentiated specimens by species (identified using COI sequences) and between lakes, correctly assigning 97.4% of homoplasmic and heteroplasmic specimens with matching mitogenomes to both species and lake of origin. The shape of putative hybrids generally resembled those of the F-type mt DNA sequence that was recovered. This study confirms that hybridization does occur between sympatric Pyganodon species. Additionally, our results reemphasize the value of modern morphometric techniques for distinguishing among species and populations with overlapping morphological variability.