Lophelia pertusa is a widespread colonial cold-water coral which can form large three-dimensional habitats for benthic communities. Although it is known to construct an aragonite skeleton with optically opaque and translucent bands, details of its biomineralized structure are unclear. New crystallographic data obtained from Lophelia pertusa using electron backscatter diffraction (EBSD) reveal a remarkably high degree of multiscale self-ordering and provide unprecedented detail on crystallographic orientations within the coral skeleton. The EBSD data unequivocally demonstrate a self-regulated architecture across a range of spatial scales, resulting in a specific structure which contributes to the physical robustness of its skeleton and an evolutionary advantage in such habitats.