Because of harsh conditions, suboptimal habitat quality and poor connectivity to other populations, plant populations at the margin of a distribution are expected to be less genetically diverse, but to be more divergent from each other than populations in the centre of a distribution. In northern Europe, northern marginal populations may also be younger than populations further to the south, and may have had less time to accumulate genetic diversity by mutation and gene flow. However, orchids have very small seeds, which are easily dispersed long distances by wind, and orchids are therefore expected to show less differentiation between marginal and central populations than other groups of seed plants. Here, we analysed whether Scandinavian populations of the tetraploid marsh orchid Dactylorhiza majalis ssp. majalis differ from Central European populations in genetic diversity patterns. A total of 220 plants from eight Central European and ten Scandinavian populations was examined for variation at five nuclear microsatellite loci, nuclear ITS and 13 polymorphic sites in noncoding regions of the plastid genome. The total genetic diversity was slightly lower in Scandinavia than in Central Europe, both in plastid and nuclear markers, but the differences were small. Also, the Scandinavian populations were less diverse and somewhat more strongly differentiated from each other than the Central European ones. Dactylorhiza majalis ssp. majalis has apparently colonized Scandinavia on multiple independent occasions and from different source areas in the south. Seed flow between Scandinavian populations has still not fully erased the patterns imprinted by early colonization. Our results suggest that marginal populations of orchids may be as important as central ones in preserving genetic diversity through Pleistocene glacial cycles. We also predict that orchids with their light seeds are better adapted than many other plants to respond to future climate changes by dispersing into new suitable areas.