We assess the potential impacts of climate change on conifer trees in Japan, by building statistical models to simulate potential ranges that are climatically suitable. We quantify the range shifts under the climate change scenarios for 2081-2100, using four modelling techniques: generalised additive models, artificial neural networks, generalised boosted models, and random forests. The results show that the altitudinal ranges may shift upwards approximately by 300m on average. Endemic sub-alpine species are most vulnerable, as more than 70% of their current ranges are projected to become unsuitable, suggesting that local extinctions may occur widely. If species are unable to migrate, more than 75% of modelled species may lose over half of their ranges, which indicates significant risks of climate change on conifer trees in Japan, and highlights urgent needs for appropriate adaptation policy measures.