The Forest Dormouse (Dryomys nitedula) is a small rodent with a wide, albeit severely fragmented distribution, ranging from central Europe to central Asia. Within the Italian region, D. nitedula populations are restricted to forested mountain areas of two largely disconnected regions, the eastern Alps and the Calabria region, where two distinct subspecies (D. nitedula intermedius and D. nitedula aspromontis, respectively) have been described on the basis of phenotypic characters (i.e., fur colour). Here we analysed D. nitedula samples from both regions, to investigate patterns of genetic divergence and phylogenetic relationship among these two populations. Genetic variation was studied at the level of one mitochondrial (cytochrome b gene) and three nuclear gene fragments (exon 1 of the interstitial retinoid-binding protein, exon 10 of the growth hormone receptor, and recombination activating gene 1). Phylogenetic analyses were performed using Maximum Likelihood and Bayesian inference methods. D. n. aspromontis and D. n. intermedius were found to be reciprocally monophyletic in all the phylogenetic analyses, and the genetic divergence observed between them at the mitochondrial CYTB gene was conspicuous (HKY: 0.044) when compared to previously observed values among many sister species of rodents. Our results clearly show that D. nitedula aspromontis is a deeply divergent, narrow endemic evolutionary lineage, and its conservation needs should be carefully evaluated in the near future. Moreover, such deep genetic divergence, together with phenotypic differentiation between D. n. intermedius and D. n. aspromontis, suggest that D. nitedula populations in southern Italy might belong to a distinct, previously unrecognized species.