Abstract: We studied the food composition of pearl oysters (Pinctada fucata) cultured in six habitats (Xincun and Lian of Hainan Province, Xuwen and Leizhou of Guangdong Province, and Bailong and Yingpan of Guangxi) by using fatty acid biomarkers. The fatty acid biomarkers indicate that diatoms, dinoflagellates/protozoa, chlorophyta/terrestrial plants particles, brown seaweed and bacteria could be the food compositions of P.fucata. The biomarker of chlorophyta/terrestrial plants (C18:2(n-6)+C18:3(n-3)) was significantly higher in Xincun (4.64%) than in the other places; the biomarkers of bacteria C18:1(n-7)/C18:1(n-9) and Odd br FAs were higher in Lian (1.29 and 4.21%) than in the others; the markers of diatoms (C16:1(n-7)/C16:0 and DHA/EPA) were significantly higher in Leizhou (1.06 and 1.13) than in the others; the biomarker of brown seaweed C20:4(n-6) was significantly higher in Bailong (9.08%) than in the others; the biomarker of dinoflagellates/protozoa (DHA) was significantly higher in Xincun, Lian, Xuwen, Bailong and Yingpan than in Leizhou. It is indicated that the food composition of the pearl oysters was closely related with their habitats.