Beech has a broad European expansion and builds its southern most populations in Greece. Three polymorphic cpDNA microsatellite primers were used to describe the variation patterns of this tree in 40 populations. As many as 13 haplotypes were identified. Most of the variation was distributed among populations, but a considerable variation was also observed within some populations. No strong spatial structure was detected suggesting complex postglacial migration patterns. Possible explanations include the existence of several separated refugia in the region, the recolonization of mountains from different beech lineages and the formation of an introgression zone between two different beech subspecies in the broader area of Rodopi.