Amorphous calcium carbonate (ACC) is a precursor phase of calcite in the formation of the sea urchin larval spicule. The goal of this research is to study the formation and stabilization mode of this transient phase. We first characterized the mineralogy of the spicules from the sea urchin Strongylocentrotus purpuratus. We then examined the role of the macromolecules extracted from the spicules at different growth stages in the formation of transient ACC in vitro. The biogenic amorphous transient phase is shown to be both structurally and compositionally different from the known stable ACC phases. It does not contain bound water, and is thus the first dehydrated ACC phase to be detected. The macromolecules that were extracted at early stages of spicule growth, when the amorphous content of the biogenic mineral is high, induced the formation of transient ACC in vitro in the presence of magnesium ions. In contrast, the macromolecules extracted at a later stage, when the spicules are completely crystalline, induced the formation of single crystals of low magnesian calcite. We therefore deduce that the macromolecules from the sea urchin larval spicules together with magnesium ions, mediate the transient formation of ACC as a precursor to calcite. These observations may well provide novel ideas for improved materials synthesis.