Future climate change is a major threat to biodiversity through habitat degradation or species geographic range shifts. The alteration of habitats under climate change could cause the current nature reserves less valuable to conserve species in the future. Forecasting the future distributions would enable us to identify priority species and areas, leading more effective conservation planning. First, we constructed species distribution models for 179 butterflies and 30 amphibians in Japan with a presence only modelling, Maxent. We then forecasted their future distributions for three time slices (2020, 2050, 2080), and under three climate change scenarios (RCP2.6, RCP4.5, RCP8.5). The future climate variables were averaged over four climate models (MIROC5, MRI-CGCM3, GHDL-CM3, HadGEM-ES) to consider model uncertainties. Based on the future distribution maps, we identified vulnerable species to future change, which rapidly and severely decline in their range size. We also identify more robust areas that will stand as hotspot until 2080 under different climate scenarios. Our results can assist in setting desirable conservation priority areas considering future uncertainties of species distribution ranges.