In the North-east (NE) Atlantic, most intertidal fucoids and warm-temperate kelps show unique low-latitude gene pools matching long-term climatic refugia. For cold-temperate kelps data are scarcer despite their unique cultural, ecological and economic significance. Here we test whether the amphi-Atlantic range of Laminaria digitata is derived from past glacial survival (and vicariance) in both NE and North-west (NW) Atlantic refugia (as suggested by niche modelling), or post-glacial (re)colonization (as suggested by low mtDNA divergence). We screened 14 populations from across the species range for 12 microsatellite loci to identify and map major gene pools and refugia. We assessed if NW Atlantic survival was supported by unique endemic variation, and if genetic diversity and structure were, as predicted from larger hindcasted glacial ranges, higher in the NE Atlantic. Microsatellite data subdivided L. digitata into three main genetic groups matching Brittany, northern Europe and the NW Atlantic, with finer-scale sub-structuring within European clusters. The relatively diverse NE Atlantic lineages probably survived the Last Glacial Maximum along unglaciated periglacial shorelines of the Armorican and Celtic Seas (Brittany cluster) and Ireland (northern European cluster), and remain well differentiated despite their relative proximity. The unique Brittany gene pool, at the contemporary European rear edge, is projected to disappear in the near future under high greenhouse gas emission scenarios. Low allelic diversity and low endemism in the NW Atlantic are consistent with recent post-glacial colonization from Europe, challenging the long-standing hypothesis of in situ glacial survival. Confusion with Hedophyllum nigripes may have led to underestimation of regional diversity of L. digitata, but also to overestimation of its presence along putative trans-Atlantic migration routes. Partial incongruence between modelling and genetic-based biogeographic inferences highlights the benefits of comparing both approaches to understand how shifting climatic conditions affect marine species distributions and explain large-scale patterns of spatial genetic structure.