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Gymnospermium is a genus of early spring-flowering tuberous herbaceous plants including c. 12 species distributed from south-eastern Europe to East Asia. For the European and Caucasian populations, different taxonomic concepts have been proposed, ranging from two to five species. We used AFLP and nuclear and plastid DNA sequences ( internal transcribed spacer and ndhF-trnL) to disentangle relationships among and spatio-temporal diversification of the European populations. Further, we were interested in their relations to the Asian G. altaicum, in which they were often included. Gymnospermium originated in the mid Miocene 16.4 Mya, when it split from Leontice in East Asia. The onset of diversification in Gymnospermium was dated to the late Miocene 11.4 Mya when East Asian species diverged from the European to Central Asian G. altaicum group. The latter started to diversify in the Pontic area in the Pliocene 4.3 Mya, coinciding with topographic and climatic changes in the Mediterranean Basin and eastern Paratethys. Both sequence and AFLP datasets inferred similar relationships, revealing two main evolutionary lineages in the G. altaicum group. Both lineages show east-west disjunctions, suggesting two separate, parallel migrations to the Balkan Peninsula. One of them gave rise to the Greek endemic G. peloponnesiacum and Pontic G. odessanum; their closest relative is G. altaicum from northern Central Asia. The second lineage includes Caucasian G. smirnovii, which is sister to Balkan G. maloi and G. scipetarum. The last two species are genetically not distinct, in line with an earlier morphological study; we thus consider G. maloi to be conspecific with G. scipetarum. Despite deep phylogenetic differentiation and biogeographical distinctness, there is little evidence for morphological divergence among the species.