Prior studies recognized the presence of a single dreissenid species in Lake Superior—the zebra mussel Dreissena polymorpha. However, taxonomic keys based on traditional shell morphology are not always able to differentiate dreissenid species with confidence. We thus employed genetic and morphological analyses to identify dreissenids in a major river-embayment of Lake Superior—the lower St. Louis River/Duluth-Superior Harbor—during 2005–2006. Our results revealed the presence of a second dreissenid species—the quagga mussel D. bugensis (alternatively known as D. rostriformis bugensis). Both species occurred in mixed clusters, in which zebra mussels outnumbered quagga mussels (20–160:1). The largest quagga mussel collected in 2005 was 26.5 mm long and estimated to be two years old, suggesting that the initial introduction occurred no later than 2003. Further monitoring is necessary to determine whether the quagga mussel will colonize Lake Superior. Our results indicate that the coupling of conventional morphological and molecular approaches is essential for monitoring dreissenid species.