Over the last few years, a significant increase of wild gilthead seabream in fisheries landings have been documented in coastal areas of the eastern Adriatic Sea. It has been suggested that rapid expansion of sea-cage farming contributes to increase of seabream populations through aquaculture escapes. The aim of this research was to assess the population genetic structure of wild and farmed populations along the eastern Adriatic coast and to investigate the impact of genetic introgression of escaped farmed seabream to wild seabream populations. To this end, a set of 21 neutral microsatellites and 3 microsatellites linked to candidate genes was used (growth hormone, GH, prolactin, PRL, receptor activity modifying protein 3, RAMP3). Wild adults demonstrated changes in genetic structure within basin in the respective sampling years and reduced connectivity with wild offspring, suggesting their temporal residency within the sampling areas of the eastern Adriatic. On the contrary, we observed a strong connection of wild seabream associated with tuna farming sites and offspring from the nearby nursery grounds indicating that the surroundings of tuna sea-cage farms could function as potential spawning grounds, which was also suggested by the Roms-Ichthyop model. A genetic database of wild and farmed gilthead seabream's genotypes was developed during the course of this study. This represents an important resource and a prerequisit for successfull identification of the animal origin as a necessary step in establishing a genetic-based escapes management startegy to control further erosion of genetic integrity.