Deep-sea corals are the main ecosystem engineers of the deep-sea, provide habitat, feeding or nursery grounds for many other species, but are among the most threatened marine habitats. Understanding connectivity of deep coral reefs, particularly the cosmopolitan Lophelia pertusa and Madrepora oculata, is essential to define effective conservation strategies. Hypotheses for gene flow of these deep-sea corals in the Atlantic include moderate to high connectivity at broad and regional scales, where ocean currents sporadically transport larvae over very large distances (thousands of km), but strong discontinuities between ocean basins caused by vicariance or local adaptation. At the local and fine scales (between and within reefs), past recolonisation and local hydrology have been identified as contributors to complex connectivity patterns, ranging from weak to strong, while substrate availability and disturbance from bottom-trawling are thought to contribute to an increase in the usually low contribution from asexual reproduction. Yet, the extent of present and past connectivity of deep coral reefs along the Atlantic and Mediterranean basins, their possible recolonisation pathways following the Last Glacial Maximum (LGM) and the location of putative glacial refugia are unknown. Here we show that L. pertusa and M. oculata subpopulations in the NE Atlantic were likely recolonised via the Mediterranean following the LGM. Furthermore, we found that the Mediterranean L. pertusa reefs (but not necessarily M. oculata) appear to have been relevant glacial refugia during the Quaternary glaciations. Our results obtained using a set of polymorphic microsatellites and sequences from the ribosomal internal transcribed spacer (ITS) reveal contrasting biogeographic histories for the two closely associated species. To better understand the observed patterns and elucidate the biogeographic history of these two corals, we are developing a genotyping-by-sequencing approach, RAD-seq, which will allow us to rapidly generate large-scale sequencing data. We aim at screening genome-wide genetic polymorphism in samples from the Mediterranean to Iceland, across over 20 sampling sites. Here we present preliminary results on our on-going population genomic analyses. We anticipate that our findings will be relevant to adequate protection measures for deep-sea corals in the North Atlantic.