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Analyses of fatty acid (FA) composition in freshwater fishes promote understanding of the potential relationship between fish health or human nutrition and specific FAs. Therefore, the chemical identity of FAs in endemic fishes must be established. Paddlefish, sauger, and white bass were collected from the Ohio River. The structural identification of esterified FAs from fish-fillet lipids was conducted using gas chromatography-mass spectrometry (GC-MS). The same 13 FAs, composing more than 90% of the mass of FAs extracted by techniques used in this research, were found in all three species examined. Carbon chain length and degree and position of unsaturation were determined from the characteristic ionization and fragmentation of FA methyl esters (FAMEs) resulting from GC-MS electron impact (EI) and chemical ionization (CI) modes. Assignment of structure to the extracted FAs required complementary interpretation of both EI and CI MS. The EI spectra observed substantiate findings reported in the literature. The novelty of this research is in the thorough interpretation of CI spectra for which less data are available. The observations reported for analyses of fishes will be useful to all researchers studying FAs regardless of sample media.