Cicerbita alpina was selected to elucidate the phylogeography of tall-herb species, an ecological group whose Quaternary history is rarely addressed. This species is a typical component of subalpine herbaceous communities in the mountains of Europe. Samples collected for this study comprised the entire range of species, with a focus on those in the Carpathians. The analysis based on AFLP fingerprinting revealed a lack of a strong phylogeographical structure implying that the different parts of the present-day range have not been isolated for a long period of time probably due to the biological characteristics of the species, such as its ability to disperse over great distances. However, the genetic structure indicates some phylogeographical trends, which may reflect traces of survival in local refugia and subsequent diversification into separate lineages during the last glacial period. Within the Carpathians, the division into the Western and South-Eastern Carpathian population groups is apparent. This division is maintained at a larger scale. In particular, the South-Eastern Carpathian group is similar to the Balkan populations, while the Western Carpathian populations are closely related to those in the Eastern Alps and Sudetes. The Scandinavian populations also have a genetic affinity with the latter group and originated from a source in the Eastern Alps or Western Carpathians, presumably via a stepping stone in a northern refugium.