Abstract: The different methods of fatty acids methyl esterification (H2SO4-methanol, KOH-methanol, BF3-methanol method) were compared in this study in order to establish the optimum for analysing by gas chromatography.The fatty acids contents of Yangtze river-coilia, East sea-coilia and Yellow river-coilia were determined using internal standard method. The recoveries of the GC method were 93% ¹08% (n =3) . 29 kinds of fatty acids were identified in three kinds of coilia ectenes, of which 27 kinds were identified in both three kinds. The P∶S values were more than 0.4 in three kinds of coilia ectenes, and the AI value was 0.47, 0.38 and 0.40, respectively.The content of monounsaturated fatty acids (MUFA) accounted for more than 50% of the total fatty acids. C16∶1and C18∶1n9c, which had significant effects respectively on flavor and nutrition, were abundant in three kinds of coilia ectenes. There were significant differences (p<0.05) in most fatty acid contents of the three kinds of Coilia ectenes. The DHA content of East sea-coilia was significantly higher (p<0.05) than that of Yangtze river-coilia and Yellow river-coilia. The East sea-coilia had comparatively higher nutritive value while the Yangtze rivercoilia had better flavor base on the fatty acids content and profile.