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The originally Pacific temperate blue mussel Mytilus trossulus and its Atlantic congener M. edulis are closely related, widespread benthic species. They can be routinely distinguished by molecular markers while reliable diagnostic morphological markers are lacking. Whenever areas of the two species overlap they fall into introgressive hybridization Historically in Northern Europe populations of M. trossulus were known to be confined to the Baltic Sea. Recently M. trossulus was found in some other regions of the Northern Europe, in particular in the White Sea it coexists with M. edulis. Here we use a set of four semidiagnostic allozyme loci to perform a detailed survey of Mytilus populations in the Kandalaksha Bay of the White Sea. We use genetic data to map the distribution of M. trossulus and M. edulis in the region (i); to evaluate the extent of hybridization between the two species (ii); to determine the micro-biotopic (substrate) preferences of genotypes; vi) study size distributions of genotypes. We also perform a morphological analysis to assess the applicability of the species discrimination by the shell character suggested earlier − the extension of the nacreous layer under the ligament on the inner shell surface. M.edulis predominated in most populations of Kandalaksha Bay, but in the very top of the Bay, in Kandalaksha harbor and surrounding waters M. trossulus prevailed. In other regions M. trossulus genotypes appeared sporadically, mainly in the area of Umba harbor. Analysis of hybridization confirmed earlier observations on bimodality of mixed populations – domination of parental species genotypes over hybrids. Mosaic distribution at the regional level is supplemented with micro-biotopical mosaicism: M. trossulus genotypes were found to be more frequent on algae substrates, while M. edulis were more common on bottom substrates. Genetic study of different size classes showed a shortage of M. trossulus among bigger mussels in mixed populations. We also found a good congruence between genetics and morphology: M. trossulus on average had a reduced nacreous layer and, hence, a persistent prismatic stripe under a ligament, while M. edulis didn’t have this stripe due to developed nacreous layer. This morphological marker thus could be used for preliminary identification of M. trossulus in the White Sea populations and for mapping two species distributions. As a conclusion, our data indicate that in the White Sea M. edulis and M. trossulus stand out as rather isolated gene pools and as morphological and ecological distinct entities.