A phylogeographic analysis of eight species complexes of European reptiles was performed using different molecular methods. While mitochondrial genes (mainly cytochrome b sequences) enabled conclusions about phylogeography and differentiation, additional application of bisexually inherited markers provided information about speciation stages. As species with similar distribution patterns in southern and Central Europe were selected, matching phylogeographic patterns are useful for drawing general conclusions:(1)The species complexes are in different stages of speciation. In some cases, cryptic species were detected.(2)Highest genetic diversity occurs in southern Europe, the Near East and the Caucasus, regions corresponding with glacial refuges in the Iberian, Apennine and Balkan Peninsulas as well as in Turkey and the Caucasus. Often, several microrefugia must have existed in close neighbourhood. Additional microrefugia were located in southern France and in the Carpathian Basin.(3)North Africa and the Middle East did not serve as glacial refuges for Central or northern European lineages and are typically inhabited by independent clades.(4)Evidence for multiple range retractions and expansions, which were postulated for the times of Pleistocene climatic oscillations, could be found in the Balkans, but in Central Europe their traces have been wiped out by the last glacial. Only the Holocene invasion has left imprints in the genomes from this area.(5)Central and northern Europe were recolonized from Balkan and Pontic refugia in the Holocene.(6)Groups from the Iberian and Apennine Peninsulas rarely conquered other regions. This limitation can be attributed to the barrier function of the Pyrenees and the Alps. © 2007 Elsevier GmbH. All rights reserved.