We examined the element pattern in the otoliths of a migratory fish species that inhabit the coastal areas in the brackish of the Baltic Sea. The northern pike (Esox lucius) show migratory behaviour, spawning in streams and rivers and foraging in the sea. We examined spawning migration in four nearby streams in the south-west part of the Baltic. Otolith analysis by microPIXE revealed unique elemental patterns (Sr, Zn, Br, Co and Mn) for the juveniles in each of the different streams. The strontium signal in the otolith of the juveniles was used as an indicator of freshwater origin and the time spent in the stream. Adult pike in their migrating spawning phase were caught in each of the streams. The elemental composition in otoliths in their freshwater phase (using juvenile pike in the streams as references) was determined. A principal component analysis showed that the elemental fingerprint during the freshwater phase several years back in time was similar for the adult fish and for juveniles inhabiting the stream today. The results indicated natal homing of the adults to a specific stream, a conclusion that was strengthened by the fact that marked fish returned to spawn over consecutive years. Anadromous pike in the Baltic Sea may thus be divided in subpopulations. The results of the study may have implications for fishery management, as pike in the Baltic Sea cannot be seen as homogenous population.