Polymerase chain reaction–restriction fragment length polymorphisms (PCR-RFLPs) and sequence analysis of noncoding regions of chloroplast DNA were used to investigate 37 populations of Eritrichium nanum covering its total distribution area, the European Alps. There was no haplotypic variation within the populations, and most haplotypes were restricted to single sites or to neighbouring populations, suggesting low levels of long distance gene flow via seeds. The present geographical distribution of haplotypes probably reflects an ancient geographical pattern within two regions in the intensely glaciated western and eastern central Alps identified as genetic hotspot areas. These two regions contained seven of the total of 11 haplotypes, including many of the most derived ones. The divergent haplotypes formed closely related groups, which supported a separate evolution of these haplotypes in these two regions and, more importantly, gave strong evidence for the in situ survival of these populations on nunataks within the western and eastern central Alps during Pleistocene glaciation. This result is in concordance with a previous study on E. nanum using nuclear markers. Only one haplotype was common and widespread throughout the distributional range of E. nanum. At the same time, it was the evolutionarily basal-most and all other haplotypes were best described as its descendants. This haplotype is hypothesized to be genetically identical to a Tertiary Alpine colonizing ancestor, whose distribution was secondarily fragmented and infiltrated by derived haplotypes originating through local mutations.