Coral skeletons are built by Ca-carbonate (calcite or aragonite) crystals that exhibit distinct morphological patterns and specific spatial arrangements that constitute skeletal microstructures. Additionally, the long-standing recognition that distinct coral species growing in similar conditions are able to record environmental changes with species-specific responses provides convincing evidence that, beyond the thermodynamic rules for chemical precipitation, a biological influence is at work during the crystallization process. Through several series of comparative structural and geochemical (elemental and isotopic) data, this paper aims to firmly establish the specific properties of the distinct major taxonomic units that are commonly gathered as deep-water “corals” in current literature. Moreover, taking advantage of recent micrometric and infra-micrometric observations, attention is drawn to the remarkable similarity of the calcareous material observed at the nanoscale. These observations suggest a common biomineralization model in which mineralogical criteria are not the leading factors for the interpretation of the geochemical measurements.