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Fatty acid composition analysis in some tissues of commercially available freshwater and marine fishes in the Kenyan waters was conducted. Four (4) fish species from Lake Naivasha; Largemouth bass or black bass (Micropterus salmoides), Common carp (Cyprinus carpio), Mirror carp (Cyprinus specularis) and Tilapia (Oreochromis leucostictus) and three (3) species from the Indian Ocean; Red snapper (Lutjanus campechanus), White snapper (Macolor niger) and Rabbit fish (Siganus ludridus)] were sampled and analyzed. GC-MS analysis was performed using a GC Voyager-800 series with Trio-01 MS detector in electron ionization (EI) mode to determine qualitatively the fatty acids composition in fish oils. The study revealed that freshwater fish contain essentially omega-6 (ω-6) fatty acids series of the polyunsaturated fatty acids (PUFA) while the marine fishes have more omega3 (ω-3) fatty acids series. The linoleic acid (LA, C18:2) was the prominent omega-6 (ω-6) fatty acid while the prominent omega-3 (ω-3) fatty acid was docosahexaenoic acid (DHA, C22:6) series. This may suggest that the dietary essential fatty acids available for marine fishes was the omega-3 polyunsaturated fatty acids which may be absent and hence unavailable for freshwater fishes Thus, the marine fish species are better providers of omega-3 fatty acids such as DHA (C22:6n-3) while the freshwater species are better providers of omega-6 fatty acids such as the linoleic acid (C18:2n-6) as well as the arachidonic acid (C20:4n-6). This study reveals that marine fish species contain appreciable levels of ω-3 polyunsaturated fatty acids and would therefore be suitable for the provision of highly unsaturated low-fat diet containing omega-3 fatty acids while freshwater fishes will provide the ω-6 fatty acids. This study however, may not explain whether the ω-3 fatty acids observed in marine fishes are derived directly from the fish diet or the fish species are good converters of the short chain ω-3 fatty acids like linolenic acid (18:3n-3) into EPA and DHA through enzyme controlled de-saturation followed by chain elongation processes.