<p>The genetic variation of the Mediterranean blue mussel, Mytilus galloprovincialis from the eastern coastline of the Adriatic Sea was investigated using polymorphic microsatellite markers. In total, 843 individuals were sampled from 18 populations representing a variety of coastal environments in Croatia, Bosnia-Herzegovina, Montenegro and Albania. Neutral loci revealed low levels of genetic structure in this continuously distributed species, while one outlier locus, MGE7, which may be under selection, provided strong evidence of genetic structure. The distribution of one of the alleles of this locus, MGE7²⁴³, was significantly correlated with latitude. A genetic seascape analysis using 9 environmental and 3 geospatial variables revealed a strong association between MGE7²⁴³ and three highly correlated environmental variables, maximum sea surface temperature, minimum salinity and maximum chlorophyll-a. This association was maintained for homozygous genotypes for the MGE7²⁴³ allele, but not for heterozygotes, providing further evidence that the locus MGE7 may be under selection or closely linked to a gene under selection. These findings highlight how previously unrecognised genetic structure can be identified through the use of genetic seascape approaches.</p>