Knowing the specific flyways of the bird populations allows us to identify critical stopover sites and foraging grounds along the migration routes, as well as wintering habitats. This information is essential for effective conservation efforts. By protecting key sites along these flyways, we can ensure that birds have safe places to rest, feed, and maintain healthy populations. Common Terns undertake long-distance migrations that span continents and cross international borders. Genetic data from Croatian Common Terns, including microsatellite loci, MHC loci and mitochondrial DNA, shows no spatial associations indicating consistent exchange of genetic material between different colonies. Despite this, light-level geolocation data, used to track migration of birds from the same colonies shows clear separation of birds into two migratory flyways, with the birds from coastal colonies using the western route (West Mediterranean, East Atlantic Ocean, Gulf of Guinea) that belongs to the East Atlantic flyway, while the birds from inland colonies migrating through the eastern route (East Mediterranean, Red Sea, Gulf of Aden, West Indian Ocean, Mozambique Channel) belonging to the Black-Sea-Mediterranean flyway. We have compared the durations of migrations and wintering periods and identified key stopover sites along both flyways. Using conductivity data, we assessed the patterns of behavior during migrations and wintering and analyzed the foraging activities of terns along both flyways. Both groups show higher foraging activity on stopovers compared to the rest of the migration, but only in autumn. Birds using the eastern flyway show highly increased foraging activities during wintering. Funding: Croatian Science Foundation (IP-2020-02-8793)