To evaluate the monophyly of Cottus and to identify species groups within the genus we generated a data set of 1914 base pairs of mitochondrial DNA (cytochrome b and ATPase 8 and 6) for 87 individuals representing 36 of the 42 currently recognized species of the genus. Both parsimony and Bayesian analyses consistently supported non-monophyly of Cottus with respect to the Baikalian sculpins and the genus Leptocottus. Analyses also supported recognition of five clades within the genus Cottus. These are referred to herein as the Cottopsis, Uranidea, Baikalian, Cottus, and Cephalocottus clades. These clades encompass all but ten recognized Cottus species, nine whose placement was uncertain in our analyses and one not included in our analyses. Lastly, we recognize a freshwater sculpin clade comprising the most speciose freshwater component of the family Cottidae.