AbstractTaxonomy of Afghan pikas Ochotona rufescens distributed in Western and Central Asia has long been debated, and the presence of cryptic diversity within the species has been suggested. In this study, we used one mitochondrial (cyt b) and six nuclear (nuDNA) markers to investigate genetic diversity within Afghan pikas O. rufescens populations based on 54 new samples from Western and Central Asia. In total, we included 200 new sequences of mitochondrial cyt b and six nuclear markers from 60 samples. Our results reveal a genetic split within Afghan pikas both in mitochondrial and nuclear markers, estimated to date back to at least 0.58 Mya, suggesting that two cryptic and isolated lineages exist among Afghan pikas in Western and Central Asia. Geographic patterns corresponding to known subspecies were largely corroborated. We hypothesize that during interglacials pikas are forced to track their habitat and move to higher elevations to avoid the desertification of the lowlands, effectively trapping them in refugia at the highest elevations. During glacials, cool climate may have created lowland habitats that pikas could tolerate, potentially allowing them to disperse between mountains. Pikas thus appear to be forced into refugia during the warmer climates of interglacials, rather than enduring ice ages in refugia, like most other organisms discussed in the context of Pleistocene refugia.