Aim Our aims were to investigate the geographical distribution, population history and demographics of the hot‐spring snake Thermophis baileyi, and to examine how the Pleistocene glacial stages and geomorphological configurations resulting from the uplift of the Tibetan–Himalayan orogen shaped the genetic diversity and evolutionary history of the species.

Location Tibetan Plateau.

Methods We surveyed potential habitat sites throughout Tibet. Sequence data were obtained for three mitochondrial markers (ND2, ND4 and cytb; 2185 bp) in 181 individuals from 18 populations across the species' distribution range. We conducted population‐genetic (samova; baps), phylogenetic (maximum likelihood; Bayesian), demographic (Tajima's D; Fu's F S ; mismatch distribution) and ecological analyses (logistic regression for presence/absence data) to examine the recent distribution, evolutionary history and diversification of the species.

Results The geographical range of T. baileyi is a restricted area between the Transhimalaya and the Himalaya, along the central part of the Yarlung Tsangpo suture zone. The divergence times of sequences matched the Guxiang glaciation (300–130 ka) and the last glacial period (70–10 ka). We observed two genetically distinct lineages north of the Yarlung Tsangpo river. These lineages are known from previous work and are largely congruent with a division across the drainage divide of the Nyainqêntanglha rift. Haplotype grouping based on cluster analysis indicated the existence of riverine migration corridors between populations.