Marine mammals and seabirds tend to exhibit high accumulations of mercury, cadmium, and selenium in their livers and kidneys. In this study, chemical forms of mercury, cadmium, and selenium accumulated in the livers and kidneys of northern fur seal (Callorhinus ursinus), Risso's dolphin (Grampus griseus), and black-footed albatross (Diomedea nigripes) were studied by extended X-ray absorption fine structure (EXAFS) spectroscopy to reveal the detoxification mechanisms of these metals. It was found that mercury and selenium exist in the form of HgSe in the liver of northern fur seal. Mercury levels were found to be higher than those of Se, based on their molar ratio, in black-footed albatross. XAFS analysis disclosed an existence of chalcogenide containing both Hg−Se and the Hg−S bonds, suggesting the existence of a solid solution Hg(Se, S) as granules in black-footed albatross. In contrast, Cd concentrations in the kidney were higher than those in the liver for northern fur seal, black-footed albatross, and Risso's dolphin. It was found that Cd was bound to sulfur, which was probably derived from the metallothionein. The Cd−O bond was observed in the tissues of northern fur seal.