The ranges of the Ozark sculpin, Cottus hypselurus, and the mottled sculpin, C. bairdi, in Missouri are unresolved. Current distributions have been based on a series of indexed morphological features and morphometric ratios that can result in taxonomic difficulties. Clarification of the distributions was sought using a molecular approach to defining distinctness and diversity of the species samples. Data were used to provide Randomly Amplified Polymorphic DNA comparisons between collections from Clear Creek, Pearson Creek, the Meramec River, Little Black River and Niangua River systems. Data analysis yielded a cladogram that revealed inaccuracies in currently accepted taxonomic relationships. The results show a monophyletic clade representing mottled sculpins from four of the sampled sites. Individuals from the Niangua River formed a separate clade consisting of Ozark sculpins. The results suggest a need for further investigation and a revised classification of the sculpins studied.