An incomplete mussel (Mytilus complex) distribution map, particularly in eastern Canada, makes it difficult to discern between phenotypically and genetically similar species. To address this, mussel DNA samples from across Québec (QC), New Brunswick (NB), Prince Edward Island (PEI), Nova Scotia (NS) and Newfoundland (NF) in eastern Canada, as well as Norway (NO), the Netherlands (NL) and Spain (ES) in Europe, were genotyped using a panel of 69 single nucleotide polymorphisms (SNPs) that originated from recent research on the population structures of Mytilus spp. in other parts of the world. These findings helped delineate M. edulis, M. trossulus, M. galloprovincialis and hybrid zones across the North Atlantic, which is valuable in understanding population dynamics within current and potential future aquaculture sites. Additionally, HiFi-sequenced samples from PEI, NS, NF and NL were consecutively mapped to the phased genome to recursively assemble a M. edulis pangenome. Subsequently, 24 resequencing samples from PEI were mapped to the pangenome to assess individual gene presence-absence variation (PAV). A high degree of PAV was identified across samples, with core and dispensable genes assessed by gene ontology to infer putative function. Ultimately, this work will help inform breeding strategies as PEI develops the first M. edulis breeding program in Canada.