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Premise of research. Even though the Balkan Peninsula is a biodiversity hot spot in southeastern Europe harboring many endemic plants, very little is known about the temporal extent of the phylogeographic history and the contemporary genetic diversity of the endemics there. Haberlea rhodopensis is one of the European Gesneriaceae species occurring in this region and represents appropriate study material to address these questions. Methodology. We generated fossil-dated molecular phylogenies (atpB-rbcL, trnH-psbA, trnLF, ITS) across the Lamiales to determine the origin and age of H. rhodopensis and conducted phylogeographic (trnH-psbA, ITS) and population genetic (ISSRs) analyses on 17 populations from Bulgaria and Greece, covering the entire distribution range of the species, to investigate their biogeographic history, present-day genetic diversity, and differentiation levels. Pivotal results. The European Gesneriaceae genera have a Tertiary origin in the early Oligocene, while the Haberlea lineage emerged in the late Oligocene. Extinctions appear to have marked the history of the genus for a long period of time, and the extant populations diverged in the late Pleistocene. A significant differentiation was apparent between populations from Bulgaria, that is, the Balkan Mountains in the north and the Bulgarian side of the Rhodopi massif in the south, but there was an even stronger differentiation between the latter and populations from Greece. This might be explained by the Rhodopi massif representing a barrier to gene flow, enforced during the Last Glacial Maximum, during which populations descended on opposing north- and south-facing mountain slopes. Conclusions. Haberlea represents an ancient lineage with recent diversification. The extant populations are of recent origin and indicate glacial refugial areas in Bulgaria and Greece. This study sheds light on historic and current phylogenetic and phylogeographic events that shaped the flora of the Balkan Peninsula, an area that has long been recognized for its species diversity and richness. Our data suggest that it may have acted as a persistent refugial area in southeast Europe since the mid-Tertiary. [ABSTRACT FROM AUTHOR]