Numerous techniques have been proposed to estimate or index cougar (Puma concolor) populations, but few have been applied simultaneously to populations with reliable estimates of population size. Between 1996 and 2003, we evaluated the relative efficacy and accuracy of multiple estimation and index techniques for populations at 2 locations in Utah, USA: Monroe Mountain and the Oquirrh Mountains. We used radiotagging followed by intensive monitoring and repeated capture efforts to approach a complete enumeration of the populations. We used these benchmarks to evaluate other population estimates (Lincoln–Petersen mark–recapture, helicopter-survey probability sampling, catch-per-unit-effort) and indices (scent-station visits, track counts, hunter harvest). Monitoring over 600 scent-station-nights using different attractants June–September in 1996 and 1997 yielded a single cougar visit. Summer track-based indices reflected a 54–69% reduction in population size on the Monroe site and a numerically stable population on the Oquirrhs, but relationships between indices and the benchmark population estimates varied among techniques. Aerial track surveys required sufficient fresh snowfall accumulations for adequate tracking coverage of a given unit, conditions that were met only once on one study site in each of 3 years. Population estimates derived from helicopter-survey probability sampling exceeded reference population estimates by 120–284%, and bootstrapped estimates of standard error encompassed 25–55% of the population estimates (e.g., 5.6 ± 1.4 cougars/100 km2). Despite poor performance in predicting cougar population sizes, track-based estimates may provide better indices for monitoring large changes in population trends (i.e., with low precision). However, we recommend using multiple indices after determination of a more rigorous initial population estimate for managing populations of conservation concern and when considering connectivity to determine potential refuge sites for regional management (e.g., management by zones).