This paper examines the genetic variability of the Pacific mussel Mytilus trossulus and an introduced Atlantic species, M. galloprovincialis, in the northwestern Sea of Japan (Peter the Great Bay and Kievka Bay). The genotyping of individuals from eight populations was carried out using eight polymorphic enzyme loci and two nuclear DNA markers (Me-5 and ITS-1,2); the occurrence frequency of parent species and their hybrids was determined. The enzyme and nuclear markers demonstrated concordant genetic variation. The genotypes of the native species M. trossulus were predominant in the samples studied. The frequency of the introduced species M. galloprovincialis in the total material was relatively low; however, it reached 42 ± 2% in samples that were collected in Possjet Bay near the town of Zarubino in a zone of active international navigation. In this area the greatest number of hybrids was found as well. It is concluded that the invasion of M. galloprovincialis in the northwestern Sea of Japan is continuing; permanent populations of this mussel appeared in Possjet Bay that were not recorded here previously.