AbstractAimThe European sturgeon, Acipenser sturio, was classified as “Critically Endangered” in 1996. Its last natural population is currently living in the Gironde Estuary (French Atlantic coastal region) but has a low level of genetic diversity and is on the brink of extinction. In order to reconstitute the genetic structure, migrations and hybridization of the species across Europe, present‐day and ancient tissues from museum specimens and archaeological remains were analysed at nuclear loci. Results obtained shed a new light on the limits of reintroduction for this species.LocationThe present and past phylogeography of A. sturio in Europe are described with living specimens from the Gironde Estuary, museum specimens (19th and 20th centuries) and archaeological remains (260–2,500 BP) from most European coasts and rivers.MethodsWe describe the current and past nuclear diversity observed at five microsatellite loci for 22 living, 42 museum and 38 archaeological specimens.ResultsThe results revealed high past allelic diversity for A. sturio in the western Mediterranean and Adriatic Sea, whereas the Atlantic and Black Sea regions were marginal areas with lower polymorphism. Acipenser sturio was subdivided into Atlantic and Mediterranean lineages, with between‐lineage intraspecific hybrid individuals and Atlantic individuals caught in the Mediterranean, evidence of ancient migrations. Finally, these nuclear data also highlight hybrids with a sibling species, the Atlantic sturgeon (A. oxyrinchus), possibly even in the last living population in the Gironde Estuary.Main conclusionsNuclear markers allowed the phylogeographic description of this sturgeon. The molecular analysis provided evidence of high past diversity in the Mediterranean and the detection of hybridization: two of the individuals analysed here (i.e. 3%) were A. sturio × A. oxyrinchus hybrids, five (8%) were found to have migrated between Atlantic and Mediterranean (individuals of Atlantic lineage captured in the Mediterranean and vice versa) and two (3%) were Atlantic–Mediterranean hybridized. Around 10% of the A sturio specimens have undergone migrations between the Atlantic Ocean and the Mediterranean Sea, new knowledge which provides valuable arguments for reintroduction plans, that is, the possible use of European sturgeons for Mediterranean stocking and of A. oxyrinchus for European stocking.