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The article presents the study conducted regarding the use of nitrogen and carbon isotope values of individual amino acids (AA) in determining the foraging ecology of the four penguin species in Southern Ocean. The study aims to identify these values of individual amino acids which isolated from the penguins' chick blood foraging in various oceanic regions. It shows that the carbon isotope values of all AAs have declined with latitude while the difference in the nitrogen isotope values of the penguins is due to the difference of their trophic levels and foraging locations. The result shows that the isotopes reflect the relative trophic level of the species.