Blue mussels (Mytilus spp.) are ecologically and economically important bivalves widespread in both hemispheres. Their relevance to coastal ecosystems and the aquaculture industry has made them extensively studied. The Mytilus complex consists of distinct genetic lineages, including Mytilus edulis, Mytilus galloprovincialis, Mytilus trossulus, and their fertile hybrids. In overlapping areas, they create complex hybrid zones, which have been investigated along European coasts, employing multi-marker approaches. However, knowledge gaps still exist in the North-east Atlantic region, in the middle of their hybrid zone around the island of Ireland, regarding their genomic composition, population structure, and connectivity. This study addresses these gaps by genotyping 781 individuals from 26 sites encompassing Ireland’s hybrid zone, including both wild and farmed stocks from varying environmental conditions. Using a selected panel of 72 SNP markers, we examined relationships among genotypic composition, genetic diversity, isolation by distance (IBD), and environmental variables to identify drivers of Mytilus genetic structure. Results confirmed two distinct genetic lineages and their hybrids, with a clear geographic pattern: the east coast of Ireland is dominated by pure M. edulis genotype populations, while the south, west, and north coasts exhibit varying degrees of admixture with M. galloprovincialis genotype. Pure M. galloprovincialis populations were identified at specific sites on the west and north coast. Sea current resistance and wave height were significant predictors for both genotype composition and genetic differentiation. This study corroborates previous findings and provides the first comprehensive investigation of Irish Mytilus spp. Population structure and connectivity using a multi-marker approach. The findings highlight the importance of understanding the Mytilus complex’s composition and population dynamics to inform sustainable aquaculture practices and monitor potential climate change-driven shifts in the North-east Atlantic region.