The edible dormouse (Glis glis), a species from a monotypic genus of family Gliridae, which has been frequently used as a model to promote the understanding of patterns of arboreal species regarding glacial oscillations. Ancient Hyrcanian forests, one of the old-growth relicts of the temperate deciduous forests worldwide has been recently documented as an important refugium during the Last Glacial Maximum (LGM). More investigation based on sequencing mitochondrial Cytb belonging to the different local populations distributed along the Hyrcanian forests as well as skull and mandible morphological assessments indicated considerable intraspecific evolutionary divergence of the species. The integration of phylogeny, geometric morphometric and environmental niche modeling approaches in this study confirms the presence of multiple cryptic refugia for fat dormice as small forest-dwelling species during paleontological oscillations