<p>Sugar kelp (<i>Saccharina latissima</i>, Phaeophyceae) is a foundation species of growing commercial interest, yet the species' population genetic structure in Atlantic Canada remains poorly resolved. A two-tiered genomic approach was used to characterize regional patterns of diversity and connectivity across the Estuary and Gulf of St. Lawrence and the coast of Nova Scotia. Reduced-representation genotyping by DArTseq provided broad spatial coverage (603 individuals, 23 sites, 4,386 SNPs), while low-coverage whole-genome sequencing (WGS) of a representative subset of populations generated high-resolution datasets using both GATK- and ANGSD-based pipelines (10⁵–10⁶ variants). Population structure was congruent across datasets. Nova Scotia populations were clearly differentiated from those in Québec, and finer-scale structure was evident among the Gaspé Peninsula, Baie-des-Chaleurs, North Shore and Miquelon. Neutral WGS datasets revealed moderate differentiation and predominantly negative F_IS values. Outlier loci showed elevated F_ST, indicating that adaptive divergence amplifies underlying demographic structure. Although DArTseq produced higher and more variable F_ST estimates, it recovered the same major groupings, underscoring robustness across marker systems. Lower diversity in estuarine populations and a higher number of private-alleles in Nova Scotia are consistent with serial founder effects during postglacial range expansion, while the Gulf of St. Lawrence likely represents a suture zone where distinct lineages have admixed. These results reveal strong, hierarchical population structure in <i>S. latissima</i> shaped by limited dispersal, environmental heterogeneity and historical colonization processes. The convergence across genomic approaches provides a robust foundation for delineating management units and supporting germplasm banking and selective breeding for sustainable kelp aquaculture in the Northwest Atlantic.</p>