BACKGROUND: In order to understand feeding ecology and habitat use of coral reef fish, fatty acid composition was examined in five coral reef fishes, Thalassoma lunare, Lutjanus lutjanus, Abudefduf bengalensis, Scarus rivulatus and Scolopsis affinis collected in the Bidong Island of Malaysian South China Sea. RESULTS: Proportions of saturated fatty acids (SAFA) ranged 57.2% 74.2%, with the highest proportions in fatty acids, the second highest was monounsaturated fatty acids (MUFA) ranged from 21.4% to 39.0% and the proportion of polyunsaturated fatty acids (PUFA) was the lowest ranged from 2.8% to 14.1%. Each fatty acid composition differed among fishes, suggesting diverse feeding ecology, habitat use and migration during the fishes' life history in the coral reef habitats. CONCLUSIONS: Diets of the coral fish species might vary among species in spite of that each species are living sympatrically. Differences in fatty acid profiles might not just be considered with respect to the diets, but might be based on the habitat and migration.