Climate changes in the Arctic are predicted to alter distributions of marine species. However, such changes are difficult to quantify because information on present species distribution and the genetic variation within species is lacking or poorly examined. Blue mussels,Mytilusspp. are ecosystem engineers in the coastal zone globally. In order to improve knowledge of distribution and genetic structure of theMytilus eduliscomplex in the Arctic, we analyzed 81 SNPs in 534Mytilusspp. individuals sampled at 13 sites to provide baseline data for distribution and genetic variation ofMytilusmussels in the European Arctic.Mytilus eduliswas the most abundant species found with a clear genetic split between populations in Greenland and the Eastern Atlantic. Surprisingly, analyses revealed the presence ofM. trossulusin high Arctic NW Greenland (77°N) andM. galloprovincialisor their hybrids in SW Greenland, Svalbard and the Pechora Sea. Furthermore, a high degree of hybridization and introgression between species was observed. Our study highlights the importance of distinguishing between congener species, which can display local adaptation and suggests that information on dispersal routes and barriers are essential for accurate predictions of regional susceptibility to range expansions or invasions of boreal species in the Arctic.