Aim In the 19th/early 20th century, overfishing caused a drastic decline and finally extinction of the local sturgeon populations in the eastern Atlantic. To date, it is not known whether it was Acipenser sturio or the primarily North American Acipenser oxyrinchus that occurred here. The aim of the study was to show the historical pattern of sturgeon distribution and their diversity in this area over the last 2500 years. This question is essential for international restoration programmes. Location North-east Atlantic. Methods The study is based on 438 archaeological sturgeon remains from the estuaries of the rivers Rhine, Ems, Weser, Elbe and Eider. All bones were analysed morphologically and in 38 cases genetically by the amplification of two mitochondrial DNA fragments. Results The data from the bones older than 1000 years show that only 1.4% derive from A. sturio. In the south, this species was slightly more frequent. From the Elbe northwards, A. oxyrinchus was for a long time by far the dominant sturgeon species. Main conclusions The genetic identification of the oldest sturgeon bone shows A. oxyrinchus occurred in the north-eastern Atlantic already 6000 years ago. Consequently, the immigration of this species from North America to Europe occurred even earlier, potentially during the last glacial. The north-south occurrence of the two sturgeon species suggests that the distribution was the result of interspecific competition under different and changing environmental conditions. As previously published, genetic data from about 100- to 200-year-old museum specimens show strong dominance of A. sturio in the North Sea area, obviously A. oxyrinchus has been replaced in the time between 1000 and 200 years ago. Therefore, the Holocene distribution of sturgeons in the northeast Atlantic had a complex pattern. Determining the ecological bases of this distribution is important for the justification and success of restoration programmes.