The fatty acids profiles in the muscles, liver and abdominal adipose of five economic fish species on the markets of Shanghai in winter and summer were examined. The five fish species studied included carnivorous marine fish (Larimichthys crocea), omnivorous marine fish (Pampus argenteus), carnivorous freshwater fish (Anguilla japonica), omnivorous freshwater fish (Oreochromis mossambicus), and herbivorous freshwater fish (Ctenopharyngodon idella). The results indicated that fatty acid profile was different among these five fish species, and it was related with the living environment and feeding habit. Saturated fatty acids (SFAs) and monounsaturated fatty acids (MUFAs) tended to accumulated in abdominal adipose and liver, where fat content was high. However, polyunsaturated fatty acids (PUFAs), n-3 PUFAs and n-6 PUFAs were not correlated with tissue fat content. The SFAs, MUFAs, PUFAs, EPA and DHA content, as well as n-3/n-6 ratio were higher in carnivorous fish (A. japonica, L. crocea, P. argenteus) than in omnivorous fish (O. mossambicus) and herbivorous fish (C. idella). The n-3 PUFAs，EPA and DHA content in the muscle of marine fish (L. crocea and P. argenteus) were higher than that of freshwater fish (O. mossambicus and C. idella). In winter, the n-3 PUFAs content in abdominal muscle of C. idella and tail muscle of O. mossambicus were higher than that in summer, as well as that in the liver of A. japonica and P. argenteus. In summary, fatty acids profiles were correlated with the species, feeding habit, living environment, type of tissues and the season. The fillets of L. crocea, P. argenteus and A. japonica have high nutritional value because of its high n-3 PUFAs content. In general, fish in winter contained higher n-3 PUFAs than summer fish, thus the nutritional value of winter fish is higher than summer fish.