Understanding disjunct distribution patterns in the Balkan Peninsula and Anatolia is important in order to reconstruct robust biogeographical hypotheses. This is instrumental in understanding the recolonization patterns of Europe during the Quaternary glaciation/interglaciation periods and the potential role of Anatolia as a refugium. Unfortunately, only a few studies have been conducted to uncover such processes. Here, we used all eight species of the genus Bornmuellera (Brassicaceae) with a scattered distribution in the Balkans and Anatolia to reconstruct its biogeographic history. We applied nuclear internal transcribed spacer (ITS) and plastid trnL-F regions and showed that 1) Bornmuellera is monophyletic and, 2) It is originated in the Pliocene in Anatolia (3.88 million years ago (mya), 3) Anatolian species are not monophyletic and, 4) Divergence between the representatives of one Anatolian lade (B. cappadocica and B. kiyakii) and the Balkan Glade coincided with the Plio-Pleistocene transition (3.2-2.6 mya).