We examined the prognosis for long-term persistence of isolated populations of cutthroat troutOncorhynchus clarki and the feasibility of using barriers to protect them from nonnative salmonids. In so doing, we estimated minimum stream lengths (MSL) required by cutthroat trout populations of varying abundances and rates of population loss to emigration and mortality. Using 2,500 individuals (>75 mm) as the target population size—corresponding to an effective population size, N_e , of 500—we estimated that more than 8 km of stream were required to maintain a population with high fish abundances (0.3 fish/m), and 25 km of stream were required to maintain a population of low abundance (0.1 fish/m). Incorporating a population loss rate of 10% increased MSL to 9.3 km for the high and 27.8 km for the low abundances. Our results suggest that many isolated populations may not persist over the long term because insufficient space exists to maintain the required N_e. Barrier construction to protect cutthroat trout from nonnative salmonids may be a necessary short-term solution, but it involves a long-term risk for maintaining viable cutthroat trout populations. We propose a watershed-based framework for cutthroat trout conservation in the central and southern Rocky Mountains that emphasizes protection of strong core populations.