The total lipid and fatty acid compositions of tissues and the stomach contents of three subtropical marine fish species, subfamily Caesioninae, Caesio diagramma and C. tile, and family Siganidae Siganus canaliculatus, were investigated to clarify the differences between these species. Triacylglycerols (TAG) were the dominant depot lipids of the three species, whereas wax esters were found as a minor component. In particular, muscle lipids were found to contain mainly glycerol derivatives such as TAG and phospholipids. The major fatty acids identified in the three species were 16:0, 18:0, 18:1 n-9, and 22:6n-3 (docosahexaenoic acid, DHA). In addition, noticeable levels of 16:1 n-7, 18:1 n-7, 20:4n-6 (arachidonic acid, AA), and 20:5n-3 (eicosapentaenoic acid) were found. DHA was the most abundant polyunsaturated fatty acid (PUFA) in the muscle and viscera lipids of the three species. The high DHA levels in the lipids of all the organs were found to be higher than those of the lipid extracted from the stomach contents of the three fishes. In addition, the specimens of S. canaliculatus contained significantly higher levels of AA in its tissues than did the other two species. A high AA content is unusual since such high levels of n-6 PUFA are rarely found in higher marine organisms. These levels may be due to its characteristic feeding pattern, because S. canaliculatus prefer and mainly feed on seaweed, which often contains high amounts of n-6 PUFA, such as linoleic acid (18:2n-6) and AA.