Effects of varying dietary protein intake on serum free amino acid (FAA) concentrations were studied in harbor seals (Phoca vitulina) fed two different prey fish diets: either exclusively low-fat, high-protein walleye pollock (Theragra chalcogramma) or high-fat, relatively high-energy-density Pacific herring (Clupea pallasi). Significant differences in FAA concentrations and patterns were observed between the two diets. All essential amino acids (EAA), except methionine and phenylalanine, and two nonessential amino acids (NEAA), glycine and tyrosine, decreased when the diet was switched from herring to pollock and increased on switching back to herring. Both total EAA concentrations and EAA : NEAA ratios decreased with the elevated protein intake typical of a low-fat pollock diet, indicating an inverse correlation between EAA concentrations and dietary protein intake levels. We propose that differing dietary protein intake, caused by differences in macronutrient composition of the two prey fish species, induced a change in protein metabolism that was reflected in blood-circulating amino acids. These findings suggest that surveys of amino acid profiles may be useful to partially determine the protein metabolic status of harbor seals.