The aim of the present study was to investigate the characteristics of gonadal fatty acid composition in 19 species of wild coral reef fish (Serranidae, Lutjanidae, Lethridae, Siganidae and Labridae) from Philippine (11 species of female) and Japanese (8 species of female and 5 species of male) waters with special attention to arachidonic acid (ArA), docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) levels and their ratios. ArA levels were always higher than EPA levels in polar lipids of all the species and in neutral lipids in 17 of the 19 species. In ovarian polar lipids of the 19 species, ArA level ranged from 6.0% to 19.4%, while EPA level ranged from 0.9% to 6.2%. Ovarian DHA level was also always higher than EPA in all the species analyzed. Consequently, ArA/EPA ratios of these species were high, unlike cold- and temperate-water species. ArA was the top fatty acid component in testis polar lipids of three Lethrinus species (21.4% to 22.9%). Thus, ArA is not a minor component, that is, the major highly unsaturated fatty acids (HUFAs) of polar lipids in all coral reef fish gonads are DHA and ArA (not EPA). The present information on gonadal fatty acid composition can be used as a guideline for advancing appropriate broodstock diets of tropical coral reef fish, emerging aquaculture commodities in developing countries.