Lophelia pertusa and Madrepora oculata are the two main species building cold-water coral reefs. Habitats within cold-water coral reefs ecosystems such as the water column, sediments, coral rubble, sponges and other corals host a diverse archaeal community. However, L. pertusa and M. oculata host, if at all, a different archaeal community. The question arises why (some) Archaea are excluded from the holobiont and whether this is potentially contributing to the success of L. pertusa and M. oculata as cold-water coral reef builders.