Yellowstone Cutthroat trout (YCT) have disappeared from more than 70% of their historic range during the past200 years. With over 350 miles of occupied habitat, the Shields River Subbasin is a rare stronghold among watersheds supporting YCT in Montana, as this species is spread throughout the basin, rather than being relegated to headwater stream reaches. Unfortunately, nonnative brook trout which outcompete YCT for food and space, have been exponentially increasing in distribution and abundance in the upper basin over the past decade and if left unchecked, could entirely displace YCT in the headwaters. This has left managers with the task of assessing the tradeoffs between improving fish passage to preserve the unique interconnected YCT population (metapopulation) versus constructing barriers to secure the YCT population in the upper basin from invasion and displacement by brook trout. To inform agency management decisions, the Wildlife Conservation Society began a multi-year fish movement study using passive integrated transponder (PIT) tags in 2011. Data suggest that brook trout abundance and distribution is increasing faster than anticipated and that management action, including the use of fish barriers, is needed to secure the upper Shields River basin from brook trout invasion and the associated consequences. Agencies are currently formulating a strategy which maintains as much connected habitat as possible while also reducing or excluding brook trout from critical habitats.