The Yellowstone River is thought to be the native home of the famous Yellowstone Cutthroat. In the early 1990's, Lake Trout were discovered in Yellowstone Lake. The Lake Trout had evidently been illegally introduced from fish taken from Lewis and Shoshone Lakes where they had been introduced by authorities in 1890. In the ensuing years, it has been estimated that up to 90% of the Cutthroat population in the lake has been decimated by the lake trout. See the article below (Return of the Yellowstone Cutthroat) for mare information on this very serious problem. Since 1994, gill nets have removed almost 3 million lake trout from Yellowstone Lake and in recent years, there appears to be a real resurgence for the Cutthroat. Many fly fishers and others that track fish populations see more and larger cutthroat caught and there is a healthy population of young fish so the future is much improved.
Yellowstone River - by Wikipedia
Return of the Yellowstone cutthroat trout - by WyoFile
DIY Guide to Fly Fishing the Yellowstone River in Montana - by DIY Fly Fishing
Yellowstone River - by Montana Trout Wranglers