Pleistocene climatic changes shaped the patterns of biodiversity in Europe and around the Mediterranean. Describing the phylogeographic structure of animal populations and inferring past population dynamics is essential to developing a framework for conservation biology in Europe. Direct persecution, habitat loss, population fragmentation, and hybridization with domesticated conspecifics, are the main threats to the survival of large mammalian species. In this paper, I will summarize the available information on phylogeography and population genetics of brown bears, wolves, wildcat, and otters in Italy and in Europe.