The common tern (Sterna hirundo) is a migratory seabird experiencing a decline in breeding pairs across several European populations due to various threats, including habitat destruction and human disturbance. This study investigates the population genetic structure and diversity of common terns sampled extensively across three European areas - Northern, Southern Inland and Southern Marine - during the breeding seasons, using 18 microsatellite markers and a mitochondrial DNA control region fragment. High genetic diversity was found in both types of markers, with the Southern Marine group showing the lowest overall diversity, although signals of possible population bottlenecks were detected in all groups. Various analyses indicated that population genetic structure was weak or absent, suggesting high gene flow among groups. The low genetic differentiation is likely influenced by distinct migration patterns, particularly between Southern Inland and Marine groups. Our results suggest that geographical distance between breeding colonies had minimal effect on population genetic structure. Further studies with tracking devices are needed to clarify how migration dynamics impacts genetic structure in common terns, while conservation efforts should focus on securing multiple breeding sites and currently unoccupied areas to increase options for habitat selection, supporting the species’ genetic diversity and long-term resilience.