The phylogeographical structure of the temperate shrub Rosa pendulina at 45 locations in Europe was studied using sequencing of a non-coding cpDNA region (trnL-trnF). Our study revealed a clear geographic structure of cpDNA haplotypes. Three main haplotypes were geographically widespread, but showed little overlap in their distributions, suggesting that postglacial expansion occurred from at least two distinct glacial refugia, probably located (1) at the edge of the Alps, N Apennines or Dinaric Alps, and (2) in the Balkan Peninsula or S Carpathians. All populations at locations in the Czech Republic and surrounding regions are of Carpathian origin. This finding disproved an Alpine origin of R. pendulina populations in the Šumava Mts (Czech Republic). A contact zone between Carpathian and Alpine migration routes of R. pendulina is probably located in the Danube valley.