Factors such as oceanographic retention, isolation by distance and secondary contact zones have, among others, been suggested to explain the low, but statistically significant, neutral population structure observed in many marine fishes. European sprat Sprattus sprattus L. is not known to display philopatric spawning behaviour or to exhibit local retention of eggs and larvae. It thus constitutes a good model for studying population structure in a characteristic small pelagic fish with high dispersal potential and an opportunistic life history. We analysed 931 specimens of sprat from 9 spawning locations in and around the North Sea and Baltic Sea area and from a geographically distant population from the Adriatic Sea. Analyses of 9 microsatellite loci revealed a sharp genetic division separating samples from the northeastern Atlantic Ocean and the Baltic Sea (pairwise ¿ = 0.019 to 0.035), concurring with a steep salinity gradient. We found, at most, weak structure among samples within the northeastern Atlantic region and within the Baltic Sea (pairwise ¿ = 0.001 to 0.009). The Adriatic Sea population was highly differentiated from all northern samples (pairwise ¿ = 0.071 to 0.092). Overall, the observed population structure resembles that of most other marine fishes studied in the North and Baltic Sea areas. Nevertheless, spatially explicit differences are observed among species, probably reflecting specific life histories. Such fine-scale population structures should be taken into account when considering complex ecosystem functions, e.g. in multispecies stock management.