Some fatty acids (FA) are specific to individual classes of organisms and attempts to trace organic materials in the ocean. Fatty acid markers have been widely used to trace or confirm predator-prey relationships so as to illustrate the key trophic linkages in the marine ecosystem. Suspended particulate matter from 0m, 75 m and 150 m were collected to better understand the fatty acid composition and its fatty acid biomarkers in the southern South China Sea. The cruise was conducted by "NanFeng" RV from February 22 to March 30, initiated by South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences. The range of FA contents were 9.9-15.65 μg/L, 10.45 -14.45 μg/L and 9.65-16.45 μg/L at 0 m, 75 m and 150 m, respectively. FA contents indicate that vertical change of FA contents was unobvious. Deep chlorophyll a (Chl a) maximum phenomenon was popular in South China Sea, thus FA/Chl a concentration varied in the water column obviously. The ratio of FA/Chl a was higher than 70 at surface and 150m layer, while lower than 30 at 75m layer (except A7). Saturated fatty acids (SFA) and mono-unsaturated fatty acids (MUFA) dominated total fatty acid contents in all SPM from each layer. Major SFA was C16:0, C18:0 and C12:0. Major MUFA were C14:1n3, C16:1n7 and C16:1n9, and major polyunsaturated fatty acids (PUFA) were C18:2n6 and C22:2n6. Principle components analysis (PCA) revealed that PC1 was positively related to C16:0, C18:0 and C20:0 concentrations, so PC1 maybe the indicator of phytoplankton and debris. PC2 may be represented the information of zooplankton. Within five FA biomarkers, C16:1n7/C16:0 was positively related to C16:1/∑FA, while negatively related to ∑C18/∑FA, so the combination of C16:1n7/C16:0 and C16:1/∑FA can be considered as FA biomarker of diatoms, and ∑C18/∑FA also can be applied to indicate dinoflagellate.