In order to predict effects of climatic change in the future on a coldwater-adapted freshwater fish, we conducted ecological niche modeling (ENM) of a boreal fish, Barbatula toni (Teleostei; Cobitoidea). ENM were performed by using MAXENT (Phillips, 2006), based on 19 climate layers from Bioclim (current and future conditions) and 3 topographic layers. The current distribution model (AUC=0.939) obtained by ENM was “projected” to future layers to estimate the future distribution model. The future distribution model shows that areas of suitable habitats (index >0.5) are reduced by 13.5% in the future. In B. toni on the Hokkaido Island, 6 genetic groups corresponding to their distribution areas (North, East1, East2, East3, West, and Teshio groups) were defined by the phylogeographic analysis based on mitochondrial DNA sequences. According to the future model, suitable habitat areas (>0.5) in eastern Hokkaido (East1, East2, and East3 groups) are reduced by 32-38% in the future. Additionally, suitable areas for northern and western Hokkaido (West, Teshio and North groups) are drastically reduced by 10-7%. Effects of climate change on population structure of coldwater-adapted fish, B. toni, are uneven among regions and are more severe in north-western half of the Hokkaido Island.