Due to progressing climate change fish stock abundance has been shifted northward in regions with suitable water temperatures. However, it is not clear whether these displacements are a result of fish migrations and colonization of new territories or if they reflect sudden growth of northern populations. In this study the population structure of Gadus morhua was assessed along a latitudinal gradient from the waters around Denmark up to the Barents Sea. Using a set of ten presumably neutral microsatellite markers, a weak but significant genetic differentiation (overall FST = 0.007; p-value = 0.001) was found among cod samples collected in the Barents Sea, the North Sea and the Øresund, a sound between the Baltic Sea and the North Sea. The latter region likely represents a boundary between habitats with different environmental conditions in terms of salt content and seasonal temperature variability, accelerating a different force of evolutionary pressure on cod in this habitat. In line with this, Øresund samples were found to be significantly differentiated from the main part of the collected material under study. Although other samples were obtained in a wide latitudinal gradient from Helgoland (≈54°N, i.e. HEL) to Svalbard (≈80°N, i.e. SVA), no significant genetic difference was detected between these geographically distant samples. The most remote population sample originating from Svalbard was surprisingly genetically homogeneous with all other groups. This may indicate a young evolutionary history of cod in these water masses, but may also be due to a certain limitation of the applied method. Moreover, life-history dependent fitness of cod connected with patterns of dispersal and migration may contribute to these findings. A multidisciplinary approach including fisheries data, otolith microchemistry and local oceanographic conditions combined with further genetic studies using markers under selection will help to unravel more details as well as the integration of respective findings.