Helianthemum nummularium is a morphologically variable species that has been subdivided into several subspecies based on indumentum characters. We investigated four of these subspecies for variation in plastid DNA and leaf and petal shape in Europe. Three size-variable mononucleotide repeat regions were amplified by means of species-specific primers and 18 combined haplotypes were identified. The highest haplotype diversity was found in the Alps and the surrounding lowland areas, whereas marginal areas such as northern Europe and the south-eastern Balkans had a lower diversity. Most of the common haplotypes were shared between subspecies and showed a geographical structuring across the range of the species, whereas geographically restricted haplotypes were found elsewhere (e.g. in the Baltic area). Leaf and petal shape descriptors could not differentiate between subspecies. The role of hybridization and introgression between post-glacial migration lineages is discussed. As an alternative hypothesis to introgression between ancient taxa, we suggest that the poor correspondence between plastid haplotype distribution and subspecies circumscription could be a result of multiple origins of similar morphs (grouped into taxonomic subspecies) in different parts of the distribution range of the complex. (c) 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176, 311-331.