The meagre Argyrosomus regius is a large Sciaenid fish known toreproduce in the eastern Atlantic and Mediterranean Sea in just five distinct andrestricted geographic areas: along the Mauritanian coast and at estuary openings (Gironde,Tagus, Guadalquivir and Nile). The biological traits of A. regius (highdispersal capabilities, high fecundity, long larval phase, overlapping generations,reproduction until 40 years of age) are, in principle, favourable to high gene flow, whichshould lead to genetic homogeneity over large geographic scales. Nevertheless, the highgeographic distances between the few reproductive areas leads one ask whether there isgenetic differentiation in this species. In the present study, the genetic differentiationof the wild A. regius was investigated across most of its natural rangefrom the Atlantic Ocean (France, Portugal, Spain, Mauritania) to the Mediterranean Sea(Egypt, Turkey), using 11 microsatellite markers previously identified in anotherSciaenid, the red drum Sciaenops ocellatus. At least two very distinctgroups could be identified, separated by the Gibraltar Strait. Genetic divergences(FST values) were intermediate between the Atlantic samples(0.012–0.041), high between Egypt and the Atlantic (0.06–0.107) or Aegean Sea (0.081) andextremely high between the Aegean Sea and the Atlantic (0.098–0.168). A. regiusexhibited a very high level of genetic differentiation rarely reported in marinefishes. These results also demonstrate the existence of a sixth independent spawning areain the Menderes delta (Turkey). Factors potentially involved in this very high geneticfragmentation are discussed, including physical barriers, glaciation pulses and biologicaltraits.