. Habitat diversity plays a significant role in shaping the genetic structure of cetacean populations. However, theprocesses involved in defining the genetic differentiation of these highly mobile marine mammals are still largelyunknown.2. Levels of genetic differentiation and dispersal patterns of common bottlenose dolphins (Tursiops truncatus)were assessed in the north-eastern Mediterranean Sea, with a focus on the Adriatic Sea. This is a regioncharacterized by diverse marine ecosystems and high levels of human-induced habitat degradation.3. Although this species seems almost uniformly distributed throughout the Adriatic Basin, genetic evidencerejected the hypothesis of a single stock. Pairwise estimates of genetic differentiation at 12 microsatellite loci,and mitochondrial DNA (entire control region, 920bp), revealed diverse levels of genetic differentiation amongfive putative populations from the Tyrrhenian Sea to the Aegean Sea.4. A fine-scale genetic structure was recorded within the Adriatic Sea, where females appear to be the principalgene flow mediators. The assessment of recent migration rates indicates a relatively high level of gene flow from theNorth Adriatic towards adjacent areas.5. Indication of a fine-scale population structure across the Adriatic Sea is a factor to be carefully considered inthe emerging marine management scenario set by the implementation of the EU Marine Strategy FrameworkDirective (2008/56/CE), particularly when it comes to assessing and managing direct mortality caused by humanactivities (e.g. fisheries or maritime traffic). A good knowledge of population structure at the basin level is alsofundamental for the identifi cation of potential Adriatic Special Areas of Conservation for the bottlenose dolphinunder the Habitats Directive (Council Directive 92/43/EEC).