ATLAS work package 1 & 4 presentation at ATLAS 3rd General Assembly. Aim: To infer cold-water corals post-glacial biogeographical history and assess the role of Mediterranean Sea glacial refugia as the origin for the recolonisation of the North-eastern Atlantic Ocean. Location: North-eastern Atlantic Ocean and Mediterranean Sea. Taxon: Lophelia pertusa, Madrepora oculata. Methods: We sampled cold-water corals using remotely operated vehicles and performed one geological corer for coral and sediment dating. We characterized spatial genetic patterns (microsatellites and a nuclear gene fragment) using networks, clustering and measures of genetic differentiation. Results: Microsatellite and sequence data were congruent, and together they showed a contrast between the two species. Populations of L. pertusa present a lack of genetic structure across the North-eastern Atlantic, a dominant pioneer haplotype, local haplotype radiations and a majority of endemic variation in lower latitudes. Surprisingly, sharply genetically differentiated population units were revealed across the North-eastern Atlantic for M. oculata. The genetic lineages are poorly admixed, even along neighbouring sites. Main conclusions: Our study shows contrasting post-glacial colonisation pathways for two main habitat-forming species in the deep-sea. The cold-water coral L. pertusa has likely undertaken a recent (post-glacial) recolonisation of the North-eastern Atlantic from Mediterranean refugial populations. Contrastingly, the strong genetic differentiation of M. oculata populations mirrors the effects of long-term isolation in multiple refugia. We suggest that these distinct and genetically diverged, refugial populations initiated the post-glacial recolonization of North-eastern Atlantic margins, leading to a secondary contact in the northern range. Incipient reproductive isolation may reduce or prevent present day gene flow among divergent but co-occurring M. oculata lineages. This study highlights the need to disentangle the influence of present day dispersal and evolutionary processes on the distribution of genetic polymorphism, to unravel the influence of past and future environmental changes on connectivity in the inconspicuous deep-sea ecosystems associated to cold-water corals.