Arabidopsishalleri,phylogeography,Carpathians,Alps,Sudetes,Harz,Quaternary,taxonomy 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 showed that two genetically different groups of populations are present in western and eastern part of the Carpathians. The hypothesis on the existence of a glacial refugium in the Western Carpathians cannot be rejected by our data. It seems, however, that evidence collected during the present study are not conclusive. The area of Bohemian Forest is another place of high genetic diversity, where the existence of a glacial refugium can be hypothesised. The area of Sudetes was colonised after LGM probably by migrants from the Bohemian Forest.