Understanding how species have responded to strong climatic fluctuations accompanying glacial-interglacial cycles is critical to predicting their likely responses to future climate change, and therefore can help guide conservation strategies. Using molecular phylogeography and ecological niche modelling, we aimed to understand how a newly recognized cryptic montane mammal (Spermophilus taurensis, Taurus ground squirrels) has responded to global climate changes through the Late Quaternary glacial-interglacial cycles as a means to better predict their likely responses to future climate change. Accordingly, 51 cytochrome b mitochondrial DNA sequences from throughout the known distribution of Taurus ground squirrels were used to investigate the intraspecific diversification. Besides molecular phylogeography, ecological niche modelling was also employed to get insights into possible climate-driven altitudinal range shifts in the past (the Last Glacial Maximum, 22 kya and the Mid-Holocene, 6 kya) and in the future (2050). Taurus ground squirrels survived the Late Quaternary glacial-interglacial cycles by altitudinal migrations without large geographical displacements. As warming occurred from the Last Glacial Maximum to the Mid-Holocene to the present, the potential distribution of Taurus ground squirrels shifted towards higher altitudes, resulting in a smaller range in the present. As warming continues, the potential distribution of Taurus ground squirrels will continue to shift towards higher altitudes, resulting in a much smaller range in the future. Particular sources of concern are the synergistic effects of future climate change and anthropogenic impacts on Taurus ground squirrels and their montane environments.