1. Continuing reductions in biodiversity, coupled with limited resources, have generated the need to perform triage to maximize success in conservation efforts.2. The development and implementation of a species recovery programme requires identifying which population units are most vulnerable to extirpation, which are most valuable to conserve, and which are most feasibly restored.3. Based on a review of the recent literature, there are few generalized approaches available to guide such prioritization procedures, but to adapt one existing method was adapted to rank populations of six imperilled, native, warmwater fish species of the Gila River basin of Arizona-New Mexico, USA and Sonora, Mexico.4. The approach uses a series of binary questions that consider the biological consequences of extinction and whose scores accumulate to rank conservation value.5. With significant adjustment, the approach accommodated differences among species, evolutionary ecologies, habitats, and conservation problems between Pacific salmon stocks (the basis of the original method) and desert fishes of the arid American Southwest. 6. A major result of the population prioritization process was that some of the highest-ranked populations have poor recovery potential, and challenges to recovery are daunting.7. Isolation management (segregation of native from non-native fishes) is considered the primary recovery action for the native fauna.8. The general method appears adaptable for application to other conservation situations and taxa, but its value will be realized only if it results in implementation of 'in-the-water' recovery actions.