We utilized summer salmonid electrofishing surveys and mitochondrial DNA analysis to study the margined sculpin (Cottus marginatus), a stream fish endemic to eastern Washington and Oregon. Our examination of margined sculpin in the Walla Walla River sub-basin yielded the first estimates of density, physical habitat characteristics and genetic diversify. Surveys of salmonids at 33 fish-bearing sites in the Walla Walla and Touchet rivers yielded 0.23 margined sculpin min-¹, possibly representing 18.9% of all fishes. The final model from a stepwise multiple regression of potential independent physical habitat variables included only boulder density and stream temperature, which were both significantly correlated with increasing catch per unit effort (r² = 0.41 and 0.20, respectively). A fish community examination via non-metric multidimensional scaling revealed consistent positive associations among catch per unit effort of margined sculpin, speckled dace (Rhinichthys osculus) and steelhead trout (Onchorhynchus mykiss). Mitochondrial DNA sequences from 20 specimens showed low genetic diversity (π < 0.01, h = 0.84) and no significant population structure (Φ_ST = 0.08) at cytochrome b, but significant diversity among 26 specimens for the non-coding control region (π = 0.02, h = 0.99, _ΦST = 0.15). Our results indicate that a single genetic lineage of margined sculpin within the Walla Walla River sub-basin was able to colonize a wide variety of microhabitats, yet inter- and possibly intraspecific interactions have allowed the accumulation of substantial genetic endemism.