Intraspecific genetic variability plays a crucial role in species’ capacity to adapt to climate change, but it is often overlooked in biodiversity impact projections, particularly for cold-water benthic environments. Here, we used molecular datasets to delimit two genetically divergent lineages within the cold-temperate kelps Saccharina latissima, Laminaria digitata, and Alaria esculenta spanning the Northeast and Northwest Atlantic. Building on such genetic insights, we employed ecological niche modelling to generate distribution projections, revealing that lineage-level models provided more realistic projections than species-level approaches. Our results identified sea-surface temperature as the dominant factor shaping kelp distribution ranges. Lineage-level projections revealed contrasting responses with a northward expansion and southern-edge contraction of habitat ranges in kelp species, leading to a net increase in the Northwest and decrease in the Northeast Atlantic. Populations of S. latissima and L. digitata on the south of c. 48°N in the Northwest (e.g., the Canadian Maritimes and Maine) and south of c. 67°N in the Northeast (e.g. France, the UK, and Germany), are projected to lose unique and endemic genetic variation. Unexpectedly, A. esculenta is predicted to lose unique genetic diversity across both Atlantic regions by the 2050s. These striking changes in distribution range and genetic characteristics highlight the necessity of conserving and managing distinct gene pools to avoid regional extinction of cold-temperate kelp forest ecosystems under ongoing climate change.