The European sardine (Sardina pilchardus) sustains some of the most important East Atlantic fisheries and is exhibiting pronounced phenotypic and distributional changes linked to environmental changes. The application of high‐resolution genomic methods is recommended to provide insights into population demographics and patterns of ecological and evolutionary diversification. This study performed genome wide SNP analysis of samples collected across understudied NE Atlantic waters as well as geographical outgroup samples from Morocco and the Western Mediterranean. The data revealed pronounced differentiation of three regional groups (NE Atlantic, Morocco, and Western Mediterranean) that can be linked to glacial vicariance and contemporary dispersal limitations. Structuring was also apparent at outlier loci adding to evidence that genome architecture and non‐neutral processes are influencing sardine populations at various spatial scales. The highly resolved Morocco group may be a previously undescribed and localized lineage and confirms complex stock structure along the North African coast. Among the NE Atlantic samples, genome wide patterns confirm restricted gene flow between Biscay and North Sea sardine with signatures of isolation by distance. FST, individual assignment, and introgression tail analyses of outlier loci revealed further structuring and identify a North Sea—Eastern Channel group distinct from a Bay of Biscay‐Celtic Sea‐Western Channel group. This pattern contradicts current management boundaries and indicates that increasing sardine numbers in the North Sea reflect an expansion of an eastern English Channel‐North Sea fringe population. While this confirms the ability of the species' northern peripheral populations to expand in response to changing conditions, the genetically differentiated southern populations may differ in this regard. Overall, this study adds to a developing genetic framework for understanding sardine biocomplexity and provides resources for management.