The wild cherry (Prunus avium L.) is considered a native species of Central European hardwoods, whereas the cultivated sweet cherry of the same botanical Classification was introduced here in Roman times. Differences in growth performance may exist between these two, therefore it is essential to certify forest reproductive material in the seed and nursery stages. We are investigating chloroplast and nuclear DNA markers for this purpose. Three chloroplast haplotypes have been identified by PCR-RFLP in the large single-copy chloroplast DNA region, to date. The most common one among these is shared by the majority of wild cherry samples collected in Austria, and a number of ancient cultivars. One more haplotype showing a number of mutations relative to the previous type is found in: two common cultivars, but also in several cherry trees in open agricultural land, previously considered as wild cherries, and in wild cherry samples from Romania and Turkey. A third haplotype was also identified in the Turkish samples. The haplotype found in the two Austrian cultivars may have been a natural introduction (overlap of different populations expanding from glacial refugia) or a remnant of ancient human introductions of cherry cultivars in Roman times, maybe tracing back to the Greek colonists on the Black Sea coast of North-East Turkey.