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Fish otoliths are continuously dsposited from fish birth to its death along with encoding environmental information. In order to decode the information, PIXE was adopted as trace elemental analysis of the otoliths. Strontium to calcium concentration ratios of red sea bream otoliths varied among rearing stations. The Sr/Ca ratios of Lake Biwa catfishes also varied between male and female and among fishing grounds. The PIXE analysis was applied to the fish stock discrimination.