Pine Creek is a large and important spawning tributary for Yellowstone cutthroat trout. Most of Pine Creek watershed is within protected national forest and the instream and riparian habitat is nearly pristine. Pine Creek is connected to the South Fork of the Snake River throughout the year, thus rainbow and hybrid trout from the South Fork of the Snake River. We sampled trout on the South Fork of the Snake River near the confluence and several sites on Pine Creek and found evidence that rainbow trout are invading the lower reaches of Pine Creek.

Many trout in the lower reach appeared to be rainbow or hybrid trout with many rainbow trout characteristics. Preliminary genetic analyses verify this observation with many trout showing mitochondrial DNA of rainbow trout with simple sequence repeat (SSR) alleles diagnostic to cutthroat trout. As we progressed upstream, fish with rainbow trout and hybrid trout coloration became less common. In the upper, headwater reaches, all trout appear to be pure Yellowstone cutthroat trout and do not show rainbow trout alleles.