ABSTRACT Aim One of the major consequences of climate change in the rapidly warming Arctic regions is the decrease in sea‐ice extent. This is accompanied by changes in marine chemistry and nutrient dynamics, which in turn drive significant shifts in ecosystems, altering their components and reshaping the interactions between them. Research on genetic differences and grasping the relevance of local adaptation is essential for deepening our knowledge of the effects of environmental changes on Arctic marine organisms, which can inform successful conservation and management. These include environmentally sensitive mussels, widely used for biomonitoring. The study aimed to examine the genetic structure and hybridisation patterns of the Mytilus species complex along the Greenland coast and identify environmental factors influencing genotypic composition or signs of local adaptation. Location The research includes three climatic zones in Greenland: high arctic, low arctic and subarctic. Extensive sampling was conducted along the understudied coast. Taxa Mytilus species complex. Methods Greenland and reference samples were successfully genotyped using a panel of 79 SNP loci, previously created and verified to distinguish Mytilus taxa and identify potential hybridisation. After filtering, 53 annotated SNPs were used to assess genetic diversity, population structure and hybridisation patterns. Regional‐scale weather and environmental proxies were obtained from online databases and used in Boosted Regression Tree analyses to identify environmental variables explaining genotypic composition. Results Most of the populations from the Greenland coast were identified as pure M. edulis . Only the Savissivik population from the north high‐Arctic region was formed by pure M. trossulus . Six populations from the north and central regions consisted of a mixture of pure M. trossulus , pure M. edulis or M. trossulus × M. edulis hybrids, mainly F1. All Greenland populations with M. edulis genomes exhibited admixtures with both American and European M. edulis , displaying a higher prevalence of the American form, except for the southern sub‐Arctic Greenland populations. Linking environmental conditions with genotypes revealed that wave exposure and food availability were most strongly associated with allele variability. Main Conclusions Large‐scale sampling along the Greenland coast revealed a taxon gradient, of M. trossulus predominating mainly in the north and M. edulis further south. M. edulis , M. trossulus and their hybrids showed non‐random distributions tied to specific niches. The admixture of M. edulis from both American and European forms suggests that Arctic coastal benthic ecosystems may serve as an important bridge facilitating connections between populations on both sides of the Atlantic. Environmental factors strongly shape the genetic structure of Mytilus spp. in Arctic coastal benthic ecosystems, while geographic location plays a minor role in allele frequency patterns. These findings align with the expectations that ocean currents around Greenland are of great importance for the population distribution of Mytilus spp., but local environmental conditions notably shape the populations' genetic structure.