Migration is one of several marine vertebrate traits increasingly affected by human encroachment. The Adriatic Sea is an important foraging and wintering site for loggerhead turtles (Caretta caretta), and one of the Mediterranean regions where they are most heavily impacted, particularly by fisheries bycatch. Conservation measures concern foraging and wintering areas and nesting grounds, and must, therefore, be informed by the natal origin of individuals in these mixed aggregates. Genetic diversity was investigated among 488 loggerheads found stranded or incidentally captured in fishing gear across the Adriatic and the origin of individuals was assessed through mixed-stock analysis based on comparison of 755 bp of mitochondrial DNA control region sequence. In addition, we highlight the importance of the Gulf of Manfredonia (Apulia, Italy), and of the northeastern Adriatic—a previously genetically undescribed foraging ground. No significant genetic divergence was recorded among sampling areas, between turtles sampled in cold and warm months or between adults and juveniles. The distribution of turtles across the Adriatic Sea appeared not to depend on individual origin. Rookeries in western Greece and Crete provided the most important contributions to the Adriatic mixed stock. In particular, the Greek populations were the most abundant locally in the Gulf of Manfredonia, so they are likely to experience an even greater impact than previously thought because of the severe fishery bycatch levels in this area. This study also provides an example of how substantial increases in sample sizes permit a relatively comprehensive testing of genetic structure across groupings in foraging aggregations.