The upper Clark Fork River basin of western Montana supports a poorly understood sculpin (Uranidea spp.) fauna that has perplexed ichthyologists and fish ecologists since the late 1800s. During our study, the basin contained three sculpin taxa whose taxonomy was under revision. All three taxa were formerly referred to the genus Cottus but are now treated as Uranidea. Our goal was to improve understanding of the distribution and ecology of two of the taxa. From 2006 to 2009, we sampled 144 reaches in 31 streams and rivers to determine distributions of each taxa across the study area and within streams. We collected habitat data in 2007 and stream temperature data from 2006–2009 to identify correlates of sculpin distributions. In streams where both taxa occurred, Rocky Mountain Sculpin Uranidea sp. cf. bairdii were downstream and Columbia Slimy Sculpin U. sp. cf. cognata were upstream with a syntopic zone in between. Summer stream temperatures strongly influenced sculpin distributions, with mean August 2007 water temperatures increasing in order of reaches characterized as: Columbia Slimy Sculpin-dominated, syntopic, Rocky Mountain Sculpin-dominated, and no sculpin. Columbia Slimy Sculpin occurred in cold tributaries of the Blackfoot, Clark Fork, and Bitterroot rivers and in two coldwater refugia in the mainstem Bitterroot River. In contrast, Rocky Mountain Sculpin occupied warmer downstream segments of many Blackfoot and Clark Fork river tributaries as well as some mainstem reaches of both rivers but were absent from the Bitterroot River drainage. Persistence of the taxa will likely depend, both directly and indirectly, on future water temperatures, and thus, sculpins are appropriate targets for researching and monitoring biological changes resulting from climate change.