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