The increasing use of phylogeographic studies, based on mitochondrial DNA, in European mammals not only provides the genetic structure of the populations and a reconstruction of the evolutionary history of each taxon but is also useful in identifying cryptic species and areas that may represent conservation priorities. We reviewed the published data (about 60 articles) reporting phylogeographic studies, based on sequences of mtDNA genes, in order to identify those populations representing putative species, not yet formally described among European mammal species of all orders, with the exception of Chiroptera. A DNA taxonomic approach and the value of subspecies are also discussed in relation to conservation activities.