Maintaining the integrity of differentiated genomes in marine organisms needs efficient isolation mechanisms, because planktonic larval dispersion provides contacts between taxa. Habitat specialisation is interesting in this respect, because it can both prevent interspecific crosses (each taxon reproduces in its own habitat) and eliminate hybrids (typically less fit than a parental taxon in each habitat). The contact zone between smooth-shelled mussels Mytilus edulis and M. galloprovincialis in Europe is a good example, as allozyme genotypes typical of both taxa seem to segregate into different habitats. However, allozymes may be selected directly and it is not known whether the same pattern can be extended to the whole genome. Here, we used 6 presumably neutral PCR markers to investigate habitat specialisation, focussing on the Bay of Quiberon, a small region in the midst of the contact zone between the 2 taxa. Confirming allozyme findings, our results indicate that habitat specialisation is apparent at the genomic scale, as M, edulis-like genotypes are found in sheltered or open-sea sites under freshwater influence, whereas M, galloprovincialis-like genotypes occupy exposed sites. Hybrid (or mixed) populations are found in open-sea or sheltered areas without freshwater influence. Therefore, habitat specialisation does contribute to the interspecific barrier. However, this mechanism seems insufficient to completely prevent the mixing of the 2 genomes, as mixed populations exist and provide opportunity for further hybridisation. Large gametic disequilibria within hybrid populations indicate the existence of restrictions to genetic exchange between the 2 taxa, even within a single habitat. Habitat-independent isolation mechanisms must, therefore, exist in addition.