Freshwater and marine cultured pearls form via identical processes to the shells of bivalves and can therefore serve as models for the biomineralization of bivalve shells in general. Their nanostructure consists of membrane-coated granules (vesicles) which contain amorphous calcium carbonate (ACC) at the beginning of the biomineralization sequence, preceding the crystallization of aragonite and vaterite. In contrast to the commonly accepted view, crystallization of ACC occurs rapidly and within the granular nano-compartments mediated by organic molecules much earlier than platelet formation. The interlamellar organic sheets in nacre that form the platelet structure of nacre themselves form by self-organization after the crystallization process of CaCO3 is completed and, thus, cannot serve as a nucleation template for aragonite. Pores in the organic sheets are postulated to be a result of this process rather than to represent the pathways for CaCO3 through pre-existing interlamellar sheets. The amorphous phase has the highest concentrations of Mg (5.8 mol%), Mn (6.6 mol%), S (4.7 mol%) and P (1 mol%) of the three CaCO3-polymorphs. Mg/Ca and Mn/Ca ratios are found to decrease in the order ACC > vaterite > aragonite, corresponding to decreasing organic content in the different phases. This, as well as an observed enrichment of Mg in the organic-rich growth-banding of the pearls, suggests an at least partially organic speciation of Mg and Mn in bivalves and may be responsible for the observed physiological influence on Mg/Ca and Mn/Ca ratios in bivalves as a proxy for environmental parameters.