Coral biomineralization typically yields either aragonite (in most scleractinians) or calcite (in octocorals), yet the drivers of this polymorph choice remain debated. Here we report a deep-sea gorgonian coral (Callogorgia sp.) with a coaxial calcite-aragonite-calcite skeleton. Growing at 1,400 m under nearly constant temperature and seawater chemistry, this specimen rules out environmental forcing as a control. High-resolution elemental mapping, Raman microscopy, and infrared nano-spectroscopy show that acidic, aspartate-rich macromolecules are enriched in the calcitic layers but depleted in the aragonitic layer. These macromolecules lower the nucleation barrier for calcite while inhibiting aragonite growth, driving abrupt, layer-by-layer phase switches. Temporal shifts in macromolecule distribution correlate with biological imprints, implying regulation via changes in calcifying tissues or symbionts. Our results provide direct in situ evidence that organic molecules, rather than external conditions, govern carbonate polymorph selection in octocorals, offering a natural template for biomimetic control of CaCO₃ phase architecture.