The extirpation of native fishes is a major concern in North America, and an understanding of population trends of imperiled fishes is critical to their management and conservation. Mountain sucker Catostomus platyrhynchus is a stream fish native to the Intermountain Region of western North America, and populations in the Black Hills of South Dakota represent the easternmost range of the species. Recently, stream surveys raised concerns about the status of mountain sucker populations in South Dakota. The purpose of this study was to document the current distribution of mountain sucker in the Black Hills of South Dakota for comparison with historic records. We analyzed stream fisheries survey data collected between 1960 and 2010 and found that mountain sucker density generally declined at three nested spatial scales: sample reach, stream, and watershed. At 14 sample reaches and two streams mountain sucker appear extirpated, whereas in remaining areas they persist in varying densities. In 2009–2010, populations exceeding densities of 0.01 fish·m−2 persisted only in Whitewood, Elk, Boxelder, and Bear Butte Creeks, and tributaries to Upper Rapid Creek. Our study documents the decline of a native fish in the Black Hills of South Dakota, and a comprehensive ecosystem management approach is needed to mitigate further loss of mountain sucker and co-occurring native species, while at the same time maintaining a highly valued non-native salmonid fishery.