Global warming is causing the distributions of many species to shift towards higher latitudes or altitudes. The white-spotted char (Salvelinus leucomaenis), a cold-water adapted stenothermal fish, is potentially vulnerable to ongoing climatic warming. We therefore evaluated the extent to which the areas protected by national parks cover current and future potential habitats of S. leucomaenis under various climate-warming scenarios. Species distribution models using MaxEnt predicted that catchment area, slope inclination, distance to the river mouth, and estimated ground water temperature were key factors for potential habitats of anadromous and landlocked populations, and that 28.4% of potential habitats would be lost with a 3°C increase in the annual average air temperature. Potential habitats at lower latitudes, in particular, are likely to be affected, and most river basin habitats would disappear if the average temperature were to increase by 2°C. Although potential habitats in higher latitudes are less vulnerable to climate warming, the current national park system would not be able to protect these refuges. There is thus an urgent need for the development of conservation measures to mitigate the potential impact of global warming on white-spotted char habitats.