Over the past 25 years, unionid mussels in the Laurentian Great Lakes of North America have been adversely impacted by invasive dreissenid mussels, which directly (e.g., by attachment to unionid shells) and indirectly (e.g., by competing for food) cause mortality. Despite the invasion, unionids have survived in several areas in the presence of dreissenid mussels. We investigated current spatial patterns in these native mussel refuges based on surveys for unionid mussels across 48 sampling locations (141 sites) in 2011 and 2012, and documented species abundance and diversity in coastal areas of lakes St. Clair and Erie. The highest-quality assemblages of native mussels (densities, richness, and diversity) appear to be concentrated in the St. Clair delta, where abundance continues to decline, as well as in in Thompson Bay of Presque Isle in Lake Erie and in just a few coastal wetlands and drowned river-mouths in the western basin of Lake Erie. The discovery of several new refuge areas suggests that unionids have a broader distribution within the region than previously thought.