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Reticulated evolution -i.e. secondary introgression/admixture between sister taxa- is increasingly recognized as a key evolutionary process that may play a role in structuring infra-specific genetic variation, and possibly promoting adaptation. Mytilus spp. is an ideal system to assess its importance, because these marine mussels form semi-isolated species that remain reproductively compatible over large time-scales. It includes three taxa that hybridize in the Northern Hemisphere (M. edulis, M. galloprovincialis and M. trossulus) and two taxa of uncertain ancestry in the Southern Hemisphere (M. platensis: South America and the Kerguelen Islands; and M. planulatus: Australasia). The Kerguelen mussels are of particular interest to investigate the potential role of admixture in enhancing micro-geographic structure, as they inhabit a small and isolated island in the Southern Ocean characterized by a highly heterogeneous environment, and genomic reticulation between Northern and Southern lineages has been suspected. Here, we extended a previous analysis by using targeted-sequencing data (51,878 SNPs) across the three Northern species and the Kerguelen population, coupled with a panel of 33 SNPs genotyped on 695 mussels across 35 sites in the Kerguelen Islands. The panel was enriched with ancestry-informative SNPs, i.e. SNPs that were more differentiated than the genomic average between Northern lineages, to evaluate whether reticulated evolution contributed to micro-geographic structure. We first showed that the Kerguelen population belongs to a divergent Southern lineage, most related to M. edulis mussels, that experienced secondary admixture with non-indigenous Northern species. We then demonstrated that the Kerguelen mussels were significantly differentiated over small spatial distance, and that this local genetic structure was associated with environmental variation and mostly revealed by ancestry-informative markers. Although local adaptation can explain the association with the environment we believe it more likely that environment variables better describe population connectivity than geographic distance. Our study highlights genetic connectivity of populations is more easily revealed by non-equilibrium secondary introgression clines at a subset of loci, while association with the environment should not be hastily advocated to support adaptation from admixture variation.