Genetic and morphometric variability in mussels are the important issues that attract the attention of numerous researchers with special emphasis in recent years on hybrid occurrence and genetic introgression. Here, the genetic and multidimensional discriminant function analysis (DFA) that included morphometric traits (MT) were performed on mussels, Mytilus trossulus and Mytilus galloprovincialis, taken from the northwestern Sea of Japan (NWSJ). The analysis, based on eight polymorphic enzyme loci and two nuclear DNA markers, used samples from eight settlements in 2011 and samples from six settlements in 2012 to 2013 for a smaller set of loci but jointly with MT analysis. If the average generation length is taken as three years, the number of immigrants (Nm) per generation was estimated approximately as Nm = 5. Assuming that interspecific gene flow is from the offspring of generations such as F₂, F₃, and F_b rather than F₁, the fraction of interspecific migrants estimated as F_b F₂ etc. are equal to 0.9% ± 0.7%. The data suggest a continuing invasion of M. galloprovincialis into NWSJ. Judging from the occurrence of hybrids of all types, it is clear that rate of genetic introgression between two taxa is at a low level, varying across 14 y in the sampled Vostok Bay area from 0% in 2012 to 2013 (this study) to 8.95% ± 1.68% back in 1999. The data support the concept of a bimodal hybrid zone, with the contact zone showing a limited degree of hybridization of two species. Analysis by DFA, using GLU-5 genotypes as a diagnostic grouping variable, allows the determination of the extent to which indigenous phenotypes and hybrids differ; M. trossulus and F1 offsprings in the 2012 to 2013 data were detected correctly with a high accuracy, near 94%. Despite that, DFA showed generally weak differentiation of settlements even with the use of a combined set of traits and indices.