Aim: Climate change threatens freshwater faunal diversity. To prioritize areas for conservation, patterns in the distribution of species must be understood. We apply genetic analysis and species distribution models to identify patterns in the distribution of freshwater amphipods around Xinjiang, China, and project the impact of climate change on endemic species.

Location: Xinjiang, China.

Methods: A time-calibrated tree containing 37 freshwater amphipod molecular samples from Xinjiang is built to calculate phylogenetic diversity, the standardized effect sizes of phylogenetic diversity, weighted endemism, and phylogenetic endemism, in 100 × 100 km grid cells. Niche differentiation among species in an area of high phylogenetic endemism is explored using n-dimensional hypervolumes and principal components analyses. Present-day and projected future suitability of habitat of endemic freshwater amphipod species is described using species distribution models.

Results: Areas of high freshwater amphipod diversity occur along the western boundary of Xinjiang; Areas north of Irtysh River, Tian Shan mountains, and the eastern margin of Pamir, have high phylogenetic endemism. Seasonal temperature and average annual water temperature contribute most to niche differentiation between geographically related freshwater species, negatively affect the projected distributions of endemic amphipods, and with continued warming, reduce future range distributions or latitudinal shifts of species.

Main Conclusions: High freshwater amphipod phylogenetic endemism occurs in Xinjiang. Environmental factors are responsible for niche differentiation of endemic species. Future climate change will substantially affect the geographic distributions of endemic amphipods. Conservation efforts should be prioritized in areas with highly concentrated phylogenetic endemism.