We explore the genetic diversity and phylogeography of the dragonflies Orthetrum cancellatum and O. coerulescens in Europe based on mitochondrial and nuclear DNA. Orthetrum cancellatum has a clear division between a group comprising Maltese, Italian, and central and northern European populations, and a group comprising mainly populations from southwestern and southeastern Europe, as well as some northern European specimens. We propose that the two groups represent two different Glacial refugia, one in the Italian Peninsula and one in the Balkans where the species survived during the Weichsel Glaciation. Orthetrum coerulescens shows a more complex pattern, although it too can be divided into two groups. One group comprise all the specimens we have identified as O. coerulescens anceps from their phenotype as well as specimens from Spain, Montenegro, and Pakistan, and some specimens from Italiy, Poland and Bulgaria. The other group comprise all other specimens from central and northern Europe, almost all specimens from Italy and Bulgaria, and all specimens from Malta. We propose that the latter group represents an Italian Glacial refugium from which the species spread to both central Europe, Malta and southern Balkan (Bulgaria) after the end of the Weichsel Glaciation. As specimens from Spain and Bulgaria, which were identified as O. coerulescens coerulescens group with specimens identified as O. coerulescens anceps we conclude that the two subspecies mix more or less freely across the Mediterranean and question the validity of two subspecies.