The Baltic Sea is a unique ecosystem and the largest body of brackish water in the world. It is inhabited by several originally freshwater fish species, one of them being pike (Esox lucius), which is adapted to the mesohaline conditions of the southern Baltic Sea and colonises its south‐western bays and lagoons. Using twelve microsatellite markers, we analysed the genetic structure of 407 Baltic Sea pike collected from ten locations in the coastal zone of the southern Baltic region and adjacent rivers and nearby lakes. We used traditional F‐statistics and a Bayesian approach implemented in STRUCTURE to investigate spatial structuring. Our results show an overall isolation by distance pattern with two distinct coastal clusters. The border area between the two clusters is characterised by a sharp salinity leap, indicating that the dispersal barrier is not physical, but physiological in nature. A third cluster was formed by three lake populations, presumably as a result of past stocking measures. Additional otolith microchemical studies demonstrate the brackish origin and residency of the majority of the pike from the coastal lagoons, supporting previous studies which suggest that the anadromous pike “ecotype” is scarce in this area of the Baltic Sea. Our results contribute to current knowledge on the population genetics of Baltic Sea pike in a previously unsampled area.

The brackish Baltic Sea is inhabited by several primary freshwater fish species. The pike (Esox lucius) is the largest of these species and acts as the top predator in the marine food web of the Baltic Sea. Prior studies have shown the importance of brackish bays as spawning grounds for the Baltic Sea pike. To identify the spawning habitat of the pike population around the island of Rügen (southern Baltic Sea)—either freshwater streams flowing into the Baltic or brackish lagoons of the Baltic—we used the ICPMS method to quantify the strontium to calcium (Sr:Ca) ratios in sagittal otoliths of 79 adult pike. In total, only six per cent (n = 5) of the analysed Baltic Sea individuals were classified as being of freshwater origin. Ninety‐four per cent (n = 74) of analysed pike were classified as having hatched in brackish water. Compared to previous studies on Baltic Sea pike, our sample shows a high proportion of pike that is of brackish origin: this highlights the adaptive capacity of this species with regard to its ability to reproduce in different salinities. Our data highlight the importance of brackish bays for pike reproduction in the southern Baltic Sea, even if pike live on the upper limit of their salinity tolerance in this area. This is an important finding considering decreases in commercial catches in the last 30 years indicating a population decline supposedly related to recruitment failures.

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