Biogenic calcites may contain considerable magnesium concentrations, significantly higher than those observed in inorganic calcites. Control of ion concentrations in the calcifying space by transport systems and properties of the organic matrix of mineralization are probably involved in the incorporation of high magnesium quantities in biogenic calcites, but their relative effects have never been quantified. In vitro precipitation experiments performed at different Mg/Ca ratios in the solution and in the presence of soluble organic matrix macromolecules (SOM) extracted from sea urchin tests and spines showed that, at a constant temperature, magnesium incorporation in the precipitated minerals was mainly dependent on the Mg/Ca ratio of the solution. However, a significant increase in magnesium incorporation was observed in the presence of SOM compared with control experiments. Furthermore, this effect was more pronounced with SOM extracted from the test, which was richer in magnesium than the spines. According to SEM observations, amorphous calcium carbonate was precipitated at high Mg/Casolution. The observed predominant effect of Mg/Casolution, probably mediated in vivo by ion transport to and from the calcifying space, was suggested to induce and stabilize a transient magnesium-rich amorphous phase essential to the formation of high magnesium calcites. Aspartic acid rich proteins, shown to be more abundant in the test than in the spine matrix, further stabilize this amorphous phase. The involvement of the organic matrix in this process can explain the observation that sympatric organisms or even different skeletal elements of the same individual present different skeletal magnesium concentrations.