1. Endangered native populations of stream salmonids in Japan face three major threats: (i) negative interactions with introduced hatchery-reared fish, (ii) fragmentation of habitat by impassable dams and (iii) recreational angling.
2. To prevent imminent extinction of many local populations, we evaluated these threats and possible conservation actions for red-spotted masu salmon (Oncorhynchus masou ishikawae) and white-spotted charr (Salvelinus leucomaenis japonicus) in the Fuji River system in central Japan.
3. Red-spotted masu salmon and white-spotted charr occupied only 0.73 and 2.4% of suitable thermal habitats, respectively, with masu salmon typically occupying habitats closer to human population centres.
4. Population viability analysis resulted in a 100-year probability of extinction of 78.1% for masu salmon and 48.1% for charr. However, extinction risk of both species was predicted to be <5% if the carrying capacity increased from 141 to 303 for masu salmon and from 94 to 125 for charr, by allowing fish passage at the lower end of the habitat, and if annual adult survival rate increased by 0.04. Adult survival rate was the principal factor associated with population persistence.
5. To conserve isolated populations of stream-dwelling salmonids, we recommend (i) assessing the distribution of remnant native and non-native fish populations, (ii) that fishing regulations are modified to improve adult survival and population persistence and (iii) that fragmented reaches be reconnected to adjacent habitat, for example by removing or modifying artificial barriers to increase the carrying capacity of the isolated populations. Reconnection of fragmented reaches should, however, be avoided if it results in non-native fish invading isolated populations.