Warm-adapted species survived the cold stages of the past glacial-interglacial cycles in southern European peninsulas and recolonized major parts of Central and Northern Europe in the wake of postglacial warming. However, many of the genetic lineages which differentiated within these refugia predate even the Pleistocene. One of these refugia is the Italian Peninsula with its surrounding islands. In this meta-analysis, we compiled phylogeographic patterns of multiple species across this region. We transformed existing geographic information on 78 animal and plant species (with a total of 471 genetic lineages) within 17 predefined areas into presence/absence matrices. We elaborated three matrices: (i) only old lineages exclusively distinguished by deep splits, (ii) only young lineages distinguished by shallow (i.e. recent) splits, and (iii) presence/absence of the respective species. To infer biogeographic relationships between the predefined areas, we performed bootstrapped neighbour joining cluster analyses on these three matrices. In addition, we reviewed the geological history of Italy to identify causes of the observed biogeographic patterns. We found Sardinia and Corsica to be biogeographically closely linked with each other, and that they diverge strongly from all other regions. Sicily also diverges strongly from all other regions, while the intra-island differentiation was comparatively low. On the Italian mainland, Calabria exhibited the most pronounced biogeographic differentiation, often with several lineages present, resulting from old vicariance events within the region. Furthermore, southern Apulia and the Po Plain with adjoining areas of northern peninsular Italy displayed considerable distinctiveness. Admixture prevailed in the areas between these three regions. The ancient isolation of Sicily, as well as Sardinia plus Corsica, resulted in endemic lineages with only moderate recent exchange with adjacent mainland regions. Pronounced diversification occurs within the Italian Peninsula. The complex tectonic activities, such as shifting (micro)plates, submergence of major parts of peninsular Italy with the genesis of numerous Pliocene islands, in combination with the climatic cycles during the Pleistocene have most likely generated the current biogeographic pattern of species. Immigrations from the Balkan Peninsula into northern Italy partly accounted for the distinctiveness of this region.