Phylogeographic analysis of Swertia perennis, a typical European subalpine springtime species, revealed the existence of at least five major phylogenetic lineages. A large phylogeographic separation exists among these geographical regions, which confirms the existence of glacial refugia in the Pyrenees, but also in the Eastern and Central Alps. The results obtained from the analyzes indicate the existence of three major differences between the populations of the Alps and the Pyrenees, but also between the populations of the Alps and those of other geographical regions (Carpathians, southern Czech Republic, Sudetes and northern Poland). The studied populations from the Black Forest and from north-eastern and southern Poland are a relic of the former wider distribution of these (periglacial) genetic groups within Swertia perennis. Our results also confirm the existence of biogeographical links between the Carpathians and the Hercynian Range and the Alps. Certainly, there was an exchange of genes between populations located in the eastern Alps, the Carpathians and the Hercynian ranges (Czech Republic, Jeseníky, Sudetes, Ore Mountains). This confirms previous results of comparative studies on the genetic diversity of populations of other vascular plant species.