Describing the chemical ontogeny of 36 specimens of Nautilus allowed the identification, as well as the determination of the relative effects, of the controls on Mg and Sr concentration in skeletal aragonite. The previously documented trend that aragonite contains higher concentrations of Sr than Mg persists within skeletal structures of Nautilus. This relationship suggests that neither physiological nor environmental controls overwhelm the mineralogical control. Significant differences in Mg and Sr concentrations of nacreous shell, prismatic shell, and septal nacre suggest that these structures may form from extracellular fluids with differing elemental concentrations. Many specimens exhibit greater variability of Mg and Sr concentrations in juvenile portions of the skeleton than in more mature portions. This suggests that either the physiochemical system matures during ontogeny and achieves increasing control over skeletal chemistry or the organism adjusts to the new conditions and behavioral maturation stabilizes elemental concentrations by reducing stress. The decreased growth rate that Nautilus experiences as it approaches maturity does not effect Mg or Sr concentrations. Differences in combined Mg and Sr concentrations among species of Nautilus indicate that extracellular fluids that produce each skeletal structure are chemically distinct, with the exception of the fluids that produced septal aragnite of N. belauensis and N. scrobiculatus, and exemplify phyletic control of trace element concentration at the species level. Although significant chemical separation exists among species of Nautilus, sufficient variation and overlap persists in elemental concentrations to make a classification based solely on these two elements ineffective. Significant chemical differences between two sympatric species of Nautilus demonstrate that physiological systems, and not environmental variables, primarily control elemental concentrations in skeletal aragonite.