The accurate identification of genetic partitioning is of primarily importance when devising conservation management strategies for today’s marine resources. The great variety of genetic structure displayed by demersal species underscores the need for the identification of common patterns that can be found across species. Here, we analyse allele frequency variation at 10 microsatellite loci of two congener demersal fish, the red mullet ( Mullus barbatus ) and the striped red mullet ( Mullus surmuletus ), from the Atlantic Ocean and the Mediterranean Sea. The results indicate that two different gene flow patterns exist between these species. The red mullet’s genetic distribution was found to be highly structured, resembling that of a metapopulation composed by independent, self-recruiting subpopulations with some connections between them. The striped red mullet displayed less genetic heterogeneity within the Mediterranean Sea and a substantial gene flow reduction between the Atlantic Ocean and Mediterranean Sea. Our results indicate that gene flow patterns in the demersal environment can be substantially different between closely related species with highly comparable biology, suggesting that biogeographic boundaries can affect demersal species in a different way despite common ecological features and spatial overlap. We conclude that the delimitation of such boundaries could be determined by the fine differences in life history traits between species.