Many marine organisms have complex genetic patterns that cannot be easily resolved by data analysis on spatial distribution of variability usually applied in population genetic studies. We propose an analytical framework to evaluate the role of dispersal during early life stages that considers the actual hydrodynamic connectivity in the Mediterranean Sea, as a factor shaping the population structure of demersal fishes. To this purpose, and to test different scenarios of gene flow, genotypes of individuals of Pagellus erythrinus sampled at 12 sites in the central Mediterranean Sea were analyzed at ten microsatellite loci. The results show the lack of genetic structure in western Mediterranean basin and a pattern of gene flow that deviates from an isolation by distance model. The observed gene flow estimates appear to be scale-dependent. At local scale, it is likely the result of multifactorial components, whereas at a larger scale it is mainly driven by the sea currents, directly influencing dispersal of larvae between sites not reachable by adult movements. Our results stress the importance of a quantitative analysis of potential early life stage dispersal in any study focusing on the population structure of fishes with a long larval stage.