Calcium carbonate exists in two main forms, calcite and aragonite, in the skeletons of marine organisms. The primary mineralogy of marine carbonates has changed over the history of the earth depending on the magnesium/calcium ratio in seawater during the periods of the so-called "calcite and aragonite seas." Organisms that prefer certain mineralogy appear to flourish when their preferred mineralogy is favored by seawater chemistry. However, this rule is not without exceptions. For example, some octocorals produce calcite despite living in an aragonite sea. Here, we address the unresolved question of how organisms such as soft corals are able to form calcitic skeletal elements in an aragonite sea. We show that an extracellular protein called ECMP-67 isolated from soft coral sclerites induces calcite formation in vitro even when the composition of the calcifying solution favors aragonite precipitation. Structural details of both the surface and the interior of single crystals generated upon interaction with ECMP-67 were analyzed with an apertureless-type nearfield IR microscope with high spatial resolution. The results show that this protein is the main determining factor for driving the production of calcite instead of aragonite in the biocalcification process and that -OH, secondary structures (e.g. ␣-helices and amides), and other necessary chemical groups are distributed over the center of the calcite crystals. Using an atomic force microscope, we also explored how this extracellular protein significantly affects the molecular-scale kinetics of crystal formation. We anticipate that a more thorough investigation of the proteinaceous skeleton content of different calcite-producing marine organisms will reveal similar components that determine the mineralogy of the organisms. These findings have significant implications for future models of the crystal structure of calcite in nature.The primary mineralogy of marine carbonates has changed over geological history depending on the magnesium/calcium ratio in seawater, including during the so-called "aragonite sea" (1) period and two periods of "calcite seas" (2). This ratio is apparently driven by changes in spreading rates along midocean ridges (1). The calcification process of aragonite and calcite mineralogy in mollusk shells (3-8) and some information about calcite (9, 10) have been reported, but our knowledge of the mechanism of the direct biological formation of calcite in marine organisms, especially in corals, remains incomplete. To develop a more complete understanding of calcite formation, detailed information concerning how biomolecules contribute to the kinetics of crystal formation, as well as the structural details of both the surface and the interior of single crystals in the submicrometer to nanometer scale must be analyzed. The mechanism of calcite formation in soft coral sclerites that we report here is completely different from the mechanisms used by other calcifying marine organisms, featuring new chemical groups and different types of single crys...