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The composition of total hydrolysable amino acids (THAAs) in a skeleton of the coral Porites australiensis, collected from Ishigaki Island, Japan, was examined in order to determine whether amino acids (AA) can be used as biomarkers of past changes in coral physiology (metabolism). Micro-samples, corresponding to a time resolution of 1 month, were collected along the growth axis of the coral. Of the 20 AAs analyzed, aspartic acid (Asp) was the most abundant, and its mole concentration relative to the sum of all other AAs (mole%Asp) showed a clear seasonal pattern of low content during winters and high during summers. A growth disturbance in the coral skeleton during 1988–1990, shown by X-ray scans and oxygen and carbon stable isotope data, was marked by a high mole%Asp ratio. Variability in carbon isotope data has often been attributed to metabolic effects, or changes in the isotopic composition of seawater, or both. The changes in mole%Asp shown here suggest that metabolic effects are mainly responsible for sharp changes in carbon isotope profiles during periods of growth disturbance.