The fatty acid compositions of the total lipid, neutral and polar lipid fractions in the liver and muscle of Capoeta sieboldii and Capoeta baliki from Todurge Lake were determined. Major fatty acids found in total lipid (TL) and neutral lipid (NL) in liver and muscles were C16:0, C16:1 n-7, C18:1 n-9, C18: 1 n-7, C20:4 n-6, C20:5 n-3, C22:5 n-3, and C22:6 n-3. Beside these acids, C18:0 was another notable fatty acid in polar lipid (PL) fraction of the tissues investigated. The n-3/n-6 ratio, which is an indicator of health benefits of fish oils, was between 2.89 (PLs of liver) and 5.84 (PLs of muscle) in C. baliki, while it was found between 1.43 (PLs of liver) and 2.52 (NLs of muscle) in C. sieboldii. C. baliki was the excellent species in terms of polyunsaturated fatty acid (PUFA) levels in TL (43.92% in muscle) and PLs (52.94% in muscle) and C22:6 n-3 amounts (docosahexaenoic acid; DHA) were responsible for these high percentages. These results suggest that Capoeta species investigated have high nutritive value in terms of polyunsaturated fatty acids for human nutrition.