There is a growing concern regarding the conservation status of amphibian species worldwide; they are more threatened and declining more rapidly than mammals or birds, and Mexico is considered one of the richest countries on Earth in terms of reptile and amphibian species. Composite models of the current distribution patterns of endemic amphibians in western Mexico were used to predict their potential distributional changes as a consequence of expected climatic changes. The models identified the most significant conservation areas within the region (hotspots), considering existing natural protected areas (NPAs) and previously recognized terrestrial priority regions for conservation (TPRCs). Three niche modelling algorithms (Bioclim, GARP and MaxEnt) used 2412 locality records for 29 species to model their climate envelopes under current and future conditions for the years 2020, 2050 and 2080. The models indicated that overall species persistence was 60% for the years 2020 and 2050, but dropped to < 20% by the year 2080. The current network of NPAs included only 8% of the areas that currently possess the greatest predicted potential richness (16–21 species), and, by 2050, the models indicate they will encompass only 3% of these areas. Six TPRCs included 44% of currently predicted areas with the highest potential species richness, but, by 2050, models predicted only 3% of such areas would persist within one TPRC. Higher uncertainty levels and variability among species surrounded the 2080 projections generated by the three algorithms. Recognition of the potential effects of climate change and consideration of the conservation value of the six TPRCs identified in this study may counteract the potential consequences of climate change on biodiversity in Mexico.