The fruticose lichen Cavernularia hultenii exhibits a strongly disjunct distribution between north-western North America, Newfoundland and north-western Europe. An investigation of its population structure, based on nuclear ITS and IGS DNA sequences, shows that western North America has a higher number of haplotypes than the two other areas. Most of the haplotypes confined to this region are rare and occur outside the area that was affected by Pleistocene glaciations. Three haplotypes are common in all three areas. The high number of haplotypes in western North America might be due to a combination of events during the Pleistocene and Holocene epochs, viz. increased lineage survival by repeated fragmentation of populations and reduced lineage extinction through rapid postglacial expansion and population growth.