The coregonine fishes from Isle Royale National Park represent a unique group that has escaped the successional changes observed elsewhere in North America. Analysis of microsatellite DNA loci revealed significant genetic differences among samples of lake whitefish (Coregonus clupeaformis) from Isle Royale, Lake Superior, and Lake Huron. The amount of genetic variation observed is consistent with that seen in other studies of whitefishes from North America. The lake whitefish from Isle Royale had previously been assigned sub-species status, but no evidence was found to support this. The effects of common ancestry and demographics both play a role in determining the relatedness of the populations. As with other fish species from Isle Royale and the upper Great Lakes, the lake whitefish have their origins in the Mississippi refugium.