At least twelve species of native cutthroat trout inhabit the western United States, three of those within the Greater Southern Rockies. The Colorado River cutthroat trout now inhabits only a few upper reaches of the Colorado River system (in northwestern Colorado and southwestern Wyoming). The Rio Grande cutthroat trout is found in a small number of higher elevation rivers in the southwestern part of Colorado and northwestern New Mexico. The Greenback cutthroat trout, currently listed as threatened under the Endangered Species Act, survives in only in small parts of the Arkansas and South Platte River systems. The yellowfin cutthroat trout was also native to Colorado but is now extinct.

All of these native cutthroat trout require clear and cold water, naturally-fluctuating stream flows, low levels of sediment, well-distributed pools, stable streambanks, and abundant stream cover. A recent report by the Western Native Trout Campaign found that most of the surviving, healthy populations of native cutthroat trout are found in designated wilderness and other roadless areas, underscoring the central role that roads play in devastating native trout populations.

Hybridization with introduced fish species is one major threat. In fact, the yellowfin cutthroat trout, originally found near the headwaters of the Arkansas River, was wiped out when rainbow trout were introduced into its Twin Lakes stronghold. Greenback cutthroat in the same area were also devastated. Road construction and use, livestock grazing, logging, mining, water diversions, and other land uses that release sediment or toxics into streams, remove trees and riparian vegetation, or pull water from streams all pose additional, severe threats to native cutthroat.

While Colorado and other states are involved in conservation efforts, the bulk of their energy has been directed at hatchery programs. Although hatchery programs are potentially an important part of recovering native cutthroat, unless trout habitat is also protected and restored the hatchery efforts will be wasted. Center for Native Ecosystems is working to protect the higher elevation habitat essential to the recovery of all three remaining native cutthroat species in the region.