The goal of this study was to examine how introduced trout influence the distributions and abundances of a sub-alpine amphibian assemblage whose members display a variety of different life-history and defence strategies. Our study was conducted in the sub-alpine lentic habitats of three wilderness areas that form the core of the Klamath-Siskiyou Bioregion of northern California, a biodiversity ‘hotspot’ that supports the highest diversity of sub-alpine, lentic-breeding amphibians in the western USA. These wilderness areas contain no native fishes, but all have been populated with non-native trout for recreational fishing. Five of the eight amphibian species that occur in this region were sufficiently common to use in our study; these included one that breeds in both temporary and permanent waters and is palatable to fish (Pacific treefrog, Pseudacris regilla), two that breed primarily in permanent waters and are unpalatable to fish (western toad, Bufo boreas, and rough-skinned newt, Taricha granulosa), and two that breed primarily in permanent waters and are palatable to fish (Cascades frog, Rana cascadae, and long-toed salamander, Ambystoma macrodactylum). Based on life histories and predator defence strategies (i.e. palatable or not), we predicted that the three palatable species would likely be negatively correlated with introduced trout, but with P. regilla less impacted because of its use of both temporary and permanent waters. We predicted that B. boreas and T. granulosa would not be significantly correlated with introduced trout due to the lack of any predator/prey interactions between them. We surveyed 728 pond, lake, or wet meadow sites during the summers of 1999–2002, using timed gill-net sets to measure trout occurrence and relative density, and visual encounter surveys to determine amphibian presence and abundance. We used semiparametric logistic regression models to quantify the effect of trout presence/absence and density on the probability of finding amphibian species in a water body while accounting for variation within and among the various lentic habitats sampled. The distributions of P. regilla, A. macrodactylum and R. cascadae were strongly negatively correlated with trout presence across all three wilderness areas. Ambystoma macrodactylum was 44 times more likely to be found in lakes without fish than in lakes with fish. Rana cascadae and P. regilla were 3.7 and 3.0 times more likely, respectively, to be found in fishless than fish-containing waters. In contrast, the two unpalatable species were either uncorrelated (T. granulosa) or positively correlated (B. boreas) with fish presence. We found that the relative density of fish (catch per unit effort) was negatively correlated with the combined abundances of the three palatable amphibians, and also with both the length and the condition of the fish themselves. Our results are consistent with a compelling body of evidence that introduced fishes greatly alter the aquatic community structure of mountain lakes, ponds, and wet meadows.