Surveys of genetic diversity patterns of self-incompatible clonal polyploid plant species are still scarcer than those of diploid plant species. Therefore, I studied the phylogeographical history of Linnaea borealis subsp. borealis to shed light on the colonization history of this clonal self-incompatible polyploid plant in Eurasia using selected regions of plastid DNA and genetic diversity patterns of 22 populations of this species employing AFLP markers. I also addressed the question of whether the genetic diversity patterns in L. borealis subsp. borealis in Eurasia are similar to those of earlier published studies of clonal self-incompatible diploid or polyploid plants. This survey revealed that the shallow phylogeographical history (six plastid haplotypes forming one haplogroup, 100% bootstrap support) and moderate genome-wide diversity estimated using AFLP markers (Fragpoly = 10.8–38.9%, I = 0.060–0.180, FST = 0.289) were general characteristics of L. borealis subsp. borealis in its Eurasian range. The sampling strategy, in most cases at 1–2-m or even 3–5-m intervals, showed that a balance between vegetative and sexual reproduction and limited pollen dispersal among compatible mates can be important for genetic diversity patterns in populations of this taxon. Despite the fact that one-half of the investigated populations were strongly isolated, they still preserved similar levels of genetic diversity across the geographical range. I found no support for the hypothesis that a bottleneck and/or inbreeding had accompanied habitat fragmentation as factors shaping genetic diversity. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173, 64–76.