By using ancient DNA methods on dry shells from museum collections, the historical phylogeography of Ostrea edulis wassuccessfully depicted in its native range for the first time. This research determines to reconstruct the historical populationstructure of the European flat oyster across Europe in the 1870s - including the now extinct Wadden Sea. The historicalphylogeography of the European flat oyster has been shaped not only by anthropogenic influences, but also by naturaldispersal ability and historical barriers to gene flow. In total, four haplogroups have been reconstructed with one haplogrouphaving a patchy distribution from the North Sea to the Atlantic coast of France. This irregular distribution could be theresult of translocations. The other three haplogroups are restricted to geographic ranges, which indicates adaptation to localenvironmental conditions or geographical barriers. They could be founder effect populations after long distance dispersals ofoysters that were constrained in their distribution to northern and southern glacial refugia in the past. The comparison withpresent-day studies on O. edulis revealed a similar population structure that indicates a temporally stable pattern over thepast 150 years despite large-scale translocations. The advantage of this historical phylogeographic study in comparison topresent-day investigations was the discovery of an autochthonous population in the German and Danish Wadden Sea in thelate 19 th century, where O. edulis is extinct today. This result provides a possible explanation for the extinction of the Europeanflat oyster in the Wadden Sea and for its constant absence until today.