The present study aimed to investigate phylogeographical patterns present within A. halleri in Central Europe, to propose hypotheses explaining the emergence of these patterns and to formulate hypotheses on the formation of the present day range of A. halleri in the region. 1281 accessions sampled from 52 populations within the investigated area were used in the study of genetic variation based on chloroplast DNA. Over 500 high quality species occurrence records were used in ecological niche modelling experiments. We evidenced the presence of a clear phylogeographic structure within A. halleri in Central Europe. Our results suggest that the species might have not survived the last glacial maximum in the Carpathians and Sudetes and that its range during the last glacial maximum might have consisted of at least two major parts: (1) a northern refugium consisting of vast refugial areas north and northeast of the Alps and (2) a southern refugium located in the Dinaric Alps and Balkan Mts. We postulate that the Sudetes and Western Carpathians were colonised mainly by plants originating from the northern refugium, whereas populations from the Eastern Carpathians originate from southern refugium. We also discuss our results in relation to the problematic taxonomy of the species. PeerJ PrePrints | https://dx.doi.org/10.7287/peerj.preprints.1259v1 | CC-BY 4.0 Open Access | rec: 22 Jul 2015, publ: 22 Jul 2015