Global climate change (GCC) significantly affects distributional patterns of organisms1, and considerable impacts on biodiversity are predicted for the next decades. Inferred effects include large-scale range shifts towards higher altitudes and latitudes2, facilitation of biological invasions3 and species extinctions1,3. Alterations of biotic patterns caused by GCC have usually been predicted on the scale of taxonomically recognized morphospecies1. However, the effects of climate change at the most fundamental level of biodiversity—intraspecific genetic diversity—remain elusive4. Here we show that the use of morphospecies-based assessments of GCC effects will result in underestimations of the true scale of biodiversity loss. Species distribution modelling and assessments of mitochondrial DNA variability in nine montane aquatic insect species in Europe indicate that future range contractions will be accompanied by severe losses of cryptic evolutionary lineages and genetic diversity within these lineages. These losses greatly exceed those at the scale of morphospecies. We also document that the extent of range reduction may be a useful proxy when predicting losses of genetic diversity. Our results demonstrate that intraspecific patterns of genetic diversity should be considered when estimating the effects of climate change on biodiversity.