From 1997-2006, we used PIT tags to determine the site fidelity of 1250 mountain yellow-legged frogs (Rana muscosa) (mylf) in the water bodies of Dusy Basin, Kings Canyon National Park during their three main activity periods of overwintering, breeding, and feeding. From the 6865 recaptures, we found mylf had more restricted distribution during breeding and overwintering, and were more widely distributed during feeding. In Dusy Basin, most breeding occurs in shallow ponds; the larger water bodies are inhabited by non-native trout preventing any successful frog breeding. Overwintering also occurs in a lake with fish. In low snowpack years, the most important breeding lake dries, and because mylf have a 3-4 year tadpole phase, all tadpole recruitment is lost. To quantify site fidelity, the tendency to return and reuse previously occupied habitats, we used multi-strata models to determine the probability of reusing the same water body (site fidelity) compared to moving and using another water body. The analysis found that mylf have strong site fidelity and the probability of returning to previously used water bodies during all activity periods was typically greater than 80% and always higher than the probability of moving to new water bodies. Frogs apparently maintain the strong site fidelity even for degraded sites, those with predatory fish or semi-perennial water bodies prone to drying. This additional impact of non-native trout relegating frog breeding to ephemeral ponds and the frog’s strong site fidelity to degraded habitats should influence future restoration strategies for this declining amphibian.