Ion micro-probe imaging of the aragonite skeleton of Pavona clavus, a massive reef-building coral, shows that magnesium and strontium are distributed very differently. In contrast to strontium, the distribution of magnesium is strongly correlated with the fine-scale structure of the skeleton and corresponds to the layered organization of aragonite fibers surrounding the centers of calcification, which have up to ten times higher magnesium concentration. This indicates a strong biological control over the magnesium composition of all structural components within the skeleton. Magnesium may be used by the coral to actively control the growth of the different skeletal crystal components.