The red deer (Cervus elaphus) is one of the most widespread and most iconic large mammal species in Europe. As both an ecological keystone species and an important game animal its genetic structure has been analysed in considerable detail over the last decade or so. Phylogeographic studies based on mitochondrial DNA have revealed three major lineages (A: western, C: eastern, B: Sardinian/North-African), interpreted as signatures of glacial refugia and postglacial recolonization routes. Until recently, however, no continent-wide nuclear genetic data were available to round off the biogeographic picture. Here, we present data from more than 600 red deer genotyped at 13 nuclear microsatellite loci and discuss them in the framework of known mtDNA phylogeography and intraspecific taxonomy (“subspecies”). We found that the nuclear genome carries a phylogeographic signal concordant with the three mitochondrial lineages, that the threatened subspecies from the Tyrrhenian islands (Sardinia, Corsica) and Mesola (Italy) are both genetically distinct and impoverished, and also present ancient DNA data from (sub-)fossil red deer remains found on the Tyrrhenian islands and the Italian mainland. The latter include the first genetic data from the extinct original Corsican population and have yielded information that the today geographically restricted B lineage once had a much wider distribution and represents an Italian refugial lineage, confirming once again that the Italian peninsula is a hotspot of unique intraspecific diversity in Europe.