The cutthroat trout (Oncorhynchus clarkii) is a popular sport fish that is native to the waters of western North America. Cutthroat trout comprises many subspecies, each of which has experienced range reduction resulting from anthropogenic activities. Hence, there is a general interest from management agencies to assess the genetic structure of managed populations of cutthroat trout subspecies to ensure that proper conservation plans are implemented. Herein, we utilize microsatellite data to characterize the genetic composition of 2 populations of Bonneville cutthroat trout in Great Basin National Park: Mill Creek and South Fork Big Wash. Mill Creek was used as a source population for reintroduction into South Fork Big Wash in the year 2000, and there is concern that South Fork Big Wash may have experienced a population bottleneck after, or during, the stocking effort. We found that both populations exhibit low genetic diversity, and that the source population, Mill Creek, exhibited mixed signals of having undergone a recent population bottleneck. Structure analysis revealed 4 distinct groups, but those groups did not segregate geographically, although a significant pairwise F_ST (0.06727, P < 0.00001) between Mill Creek and South Fork Big Wash populations suggests that some genetic differentiation has occurred.