The Northern pike (Esox lucius) is an important predator in freshwater and brackish water environments. In the Baltic Sea, Northern pike follows isolation by distance pattern across wide geographical scale. However, relatively little is known about the fine-scale population divergence and temporal genetic variation of Baltic pike, especially for populations inhabiting the eastern part of the Baltic Sea. Here, we characterize the population genetic structure of Northern pike and its temporal stability in six freshwater and one brackish water locations on the Island of Saaremaa (Estonia). To accomplish this, we collected 274 young-of-the-year (YOY) of two consecutive cohorts and 218 older specimens that were genotyped using ten microsatellite loci. Our results indicate a temporally stable population differentiation between geographically close locations and reduced diversity of the north-western Saaremaa populations. Furthermore, the correspondence analysis and a discriminant analysis of principal components showed a clear differentiation between north-western and the Gulf of Riga spawning grounds. Our findings support the idea that natal homing behavior, limited dispersal and facultative anadromy in Baltic pike likely promotes the existence of temporally stable genetic divergence among different populations at small geographical scale, representing an essential prerequisite for development of local adaptations. Thus, conservation, management and restoration efforts of coastal Baltic Sea pike should preserve the existing genetic differences between different populations and avoid actions, which potentially increase genetic homogenization.