A great help in determining the impact of future climate and environmental changes on populations can be provided by studies of past analogues, so ancient DNA (aDNA) isolated from fossil specimens is an invaluable source of genetic information about the past, which is wiped out in present DNA. Particular species can response differently to climate changes. Thus, generalisations of the climate influence can be incorrect and gathering data on individual species is essential. One of interesting species in this context is the European snow vole Chionomys nivalis, a rodent, which is a glacial relict with a fragmented distribution in mountainous parts of south-eastern Europe as well as south-western Asia. This species was much more diversified in the past and its many morphospecies were described. We will study mitochondrial (mtDNA) genomes and selected nuclear markers of fossil and contemporary specimens from the broad geographic range. The genetic results will be set in the time scale using radiocarbon dating and confronted with palaeoclimatic data. We will perform phylogeographic analyses to verify if the genetic and morphological variations are associated with the climatic and environmental changes. Specifically, we will investigate the genetic variation of the Pleistocene C. nivalis to reconstruct its origin, population dynamics, migration routes and extinctions in relation to climate changes. Comparison of phylogenies based on mtDNA and nuclear markers enables to check a potential introgression of mtDNA between C. nivalis subspecies or differential lineage sorting of mitochondrial and nuclear haplotypes. Due to specific rocky habitats occupied by C. nivalis associated with colder and arid conditions, it is interesting to check if alterations in the Pleistocene climate are also reflected in genetic variation recorded in fossils. The inclusion of fossils can help to verify if the present discontinuity in the geographic distribution of C. nivalis resulted from a recent fragmentation of one big population accompanied by geographical isolation or these particular populations originated separately from already diversified groups, e.g. in refugia during the Last Glacial Maximum. Intraspecific morphological variation in C. nivalis coincides with its phylogeographic structure based on genetics. It indicates a concordance between the morphological and molecular evolution, which is not common in other species. Thus, analyses of C. nivalis offer a promising opportunity to compare directly the morphological and genetic variation. It is interesting to check if the teeth morphology, including fossil samples, corresponds to genetic relationships and results from the former population division and long-term isolation or is rather associated with environmental factors and evolved convergently in separate lineages. Examination of aDNA can also help to assess validity of fossil subspecies determined solely on the morphology and provide the most versatile way to reconstruct evolutionary history of this species. The result will have consequences on interpretation of other rodent fossils, which are dominated component of the Pleistocene fauna. Obtained results can be a good reference point and working model for other mammals, which were widespread in the Pleistocene and survived to the present as glacial relics. The study can be helpful in research of present species that are also subjected to drastic changes of climate and environment. C. nivalis is especially interesting because its habitats lie in rocky areas in high mountains, which are most vulnerable to global warming. Accordingly, this species occurred very useful as an appropriate bioindicator in monitoring the environmental impact in mountain areas. Our study of fossil samples gives more reliable data about the climate influence on this species through a long time since at least 50,000 years. We have already obtained complete mtDNA from 5 ancient C. nivalis specimens from the Late Glacial site Obłazowa cave. Phylogenetic analyses revealed a clear phylogeographic pattern because most mitochondrial lineages were associated with certain geographical regions. The fossil samples cluster with a present day sample from Slovakia. This result suggests that the Central European population can have continuity with an older Pleistocene population. The project is an interdisciplinary approach that will involve a fruitful integration of various disciplines: genetics, palaeontology and palaeoecology.