The exotic parasite Myxobolus cerebralis was first detected in native adult Yellowstone cutthroat trout Oncorhynchus clarkii bouvierii from Yellowstone Lake in 1998, seriously threatening the ecological integrity of this pristine, naturally functioning ecosystem. We immediately began to assess the prevalence and spatial extent of M. cerebralis infection in Yellowstone cutthroat trout within Yellowstone Lake and to determine the infection risk of age-0 Yellowstone cutthroat trout, the relative abundance and actinospore production of lubificid worms, and the basic environmental characteristics of tributaries. During 1999-2001, juvenile and adult Yellowstone cutthroat trout were infected throughout Yellowstone Lake; the highest prevalence (15.3-16.4%) occurred in the northern and central regions. Exposure studies in 13 streams indicated that Pelican and Clear creeks and the Yellowstone River were positive for M. cerebralis; the highest prevalence (100%) and severity was found in Pelican Creek during mid-July. Sexually mature individuals of the oligochaete Tubifex tubifex were most abundant in early summer, were genetically homogenous, and were members of a lineage known to produce moderate to high levels of M. cerebralis triactinomyxons. Only 20 of the 3,037 sampled tubificids produced actinospores after 7 d in culture, and none of the actinospores were M. cerebralis. However, one non-actinospore-producing T. tubifex from Pelican Creek tested positive for M. cerebralis by polymerase chain reaction. Stream temperatures at Pelican Creek, a fourth-order, low-gradient stream, were over 20??C during the first exposure period, suggesting that T. tubifex were capable of producing triactinomyxons at elevated temperatures in the wild. Although the infection of otherwise healthy adult Yellowstone cutthroat trout within Yellowstone Lake suggests some resistance, our sentinel cage exposures indicated that this subspecies may be more susceptible to whirling disease than previous laboratory challenges have indicated, and M. cerebralis may be contributing to a significant recent decline in this population. ?? Copyright by the American Fisheries Society 2006.