The rainbow darter Etheostoma caeruleum is a small fish in the perch family (Percidae) that is adapted to fast-flowing streams in eastern North America. It is relatively sensitive to habitat degradation and is widely used as a sentinel of stream condition. To provide a complementary tool for assessing the integrity of stream ecosystems, 16 highly polymorphic tetranucleotide microsatellite markers were identified for these darters. Between four and 16 loci were found to be useful in five congeneric species. These markers will be useful for characterizing population genetic structure and diversity of rainbow darters and related fishes.