Mitochondrial cox1 sequencing datasets, cox1 haplotype sequences and microsatellite genotyping datasets for Saccharina latissima (3 files in total); mitochondrial cox1 sequencing datasets, cox1 haplotype sequences and microsatellite genotyping datasets for Laminaria digitata (3 files in total); cox1 sequencing datasets, cox1 haplotype sequences and mitochondrial SNP genotyping datasets for Alaria esculenta (3 files in total).

Intraspecific genetic variability matters for species adapting to climate change and yet it is generally overlooked in projections of biodiversity impacts, particularly for cold-water benthic environments. Here, we used molecular datasets to delimit two divergent genetic lineages between the Northeast and Northwest Atlantic for the cold-temperate kelps <i>Saccharina latissima</i>, <i>Laminaria digitata</i> and <i>Alaria esculenta</i>. Building on such genetic insights, we applied ecological niche modelling and found that lineage-level modelling provided more realistic projections than species-level and identified sea-surface temperature as the dominant factor shaping kelp distribution ranges. Lineage-level projections revealed distinct northward expansion and southern-edge contraction of habitat range in the Northwest vs. the Northeast Atlantic in each kelp species, leading to a net increase in the Northwest and decrease in the Northeast Atlantic, respectively. Many populations of <i>S. latissima</i> and <i>L. digitata</i> on the south of <i>c.</i> 48°N in the Northwest (e.g. the Canadian Maritimes and Maine) and those on the south of <i>c.</i> 67°N in the Northeast Atlantic (e.g. France, the UK, and Germany), are projected to lose unique and endemic genetic variation. Unexpectedly, <i>A. esculenta</i> is predicted to lose unique genetic diversity on both sides of the North Atlantic in the 2050s. These striking changes in distribution range and genetic characteristics highlight the necessity to conserving and managing distinct gene pools to avoid regional extinction of cold-temperate kelp forest ecosystems under climate change.