Marine turtles have been traditionally considered model organisms to study sex-biased behaviour and dispersal. Although female philopatry has been identified in the loggerhead turtle, with adult females returning to specific locations to nest, studies on the philopatry and breeding migrations of males remain limited. In this study we analysed 152 hatchlings using 15 microsatellite markers. Each individual came from a different nest from samples taken at 8 nesting grounds in the Mediterranean. Our results revealed the existence of 5 genetically differentiated units, mostly due to restricted gene flow for both sexes. This supports existing satellite tracking studies that suggest that mating occurs close to nesting grounds in this region. The 5 management units identified within the Mediterranean included nesting grounds from (1) Libya and Cyprus, (2) Israel, (3) Lebanon, (4) Turkey and (5) Greece. The genetic similarity between distant nesting areas (i.e. Libya and Cyprus) suggests the presence of a more complex pattern of breeding behaviour. Three possible hypotheses, that remain to be tested in future studies, could explain this result: (1) mating might take place in common foraging grounds; (2) mating could occur en route while migrating to/from the breeding grounds; or (3) recent colonisation events could connect the 2 nesting grounds. Overall, our work suggests that widespread male-mediated gene flow between loggerhead nesting grounds is likely to have been previously overstated although opportunistic breeding patterns might connect some widely separated areas.