A prerequisite in fisheries management is to identify biological meaningful delineations of stocks, the fundamental exploited units. The European anchovy is one such species in need to better identify stock boundaries. Indeed, despite a spawning aggregation behaviour both in the southern Bay of Biscay and southern North Sea in spring and summer, it has a seemingly continuous distribution in autumn across a broad region ranging from the Bay of Biscay to the northern North Sea including the English Channel, thus with potential mixing of the spawning units. We therefore used genetic markers (single nucleotide polymorphisms) to quantify the degree of gene flow between the currently managed fish stock of the bay of Biscay and northern areas of European anchovy’s distribution. Our results confirm the clear distinction between the Bay of Biscay and northernmost populations, with assignment of all English Channel samples to the latter. We also found a clear overall pattern of isolation by distance that resulted primarily from an increasing differentiation with geographic distance in the Northern group magnified by the lack of gene flow with the anchovies of the Bay of Biscay. The small reduction in gene diversity towards northern latitudes may indicate partial isolation of the leading-edge component of the Northern population. Quotient plots relating anchovy’s distribution to environmental covariates showed that anchovies sampled in autumn in the English Channel originate from the summer spawning aggregation in the warm, low saline and plankton rich south-eastern North Sea. This change in the seasonal distribution of the northern population mimics, but in opposite direction, the one of the Bay of Biscay where anchovy spread towards the north from the spawning habitat in the south-eastern bay. The encounter, without mixing, of the two populations west of Brittany in autumn suggests strong spawning site fidelity. Finally, we identified for the first time anchovies belonging to the estuarine ecotype in the Loire estuary. Our results therefore support current management units, yet with some uncertainties for the catches in the transition zones between the Bay of Biscay and the English Channel, and within river plumes in the vicinity of estuaries hosting the estuarine ecotype.