Food sources of three filter-feeding bivalves from two habitats (intertidal oyster Crassostrea gigas, mussel Mytilus galloprovincialis, and subtidal cultured scallop Chlamys farreri) of Jiaozhou Bay (Qingdao, China) were determined by fatty acid and stable isotope analysis. Cultured scallop was characterized by significant diatom markers such as 16:1/16:0 close to 1 and high ratio of 20:5(n − 3)/22:6(n − 3), hence we assume that the scallop mainly feeds on diatoms. Fatty acid biomarkers specific to bacteria and terrestrial materials were also found in considerable amounts in scallop tissue, which suggested that there were substantial bacterial and terrestrial input into the food of the species. Intertidal oyster and mussel, however, exhibited significant flagellate marker, 22:6(n − 3), and lower level of diatom markers, which indicated that flagellates are also part of intertidal bivalves’ planktonic food sources; meanwhile, high level of Chlorophyta fatty acid marker, Σ18:2(n − 6) 18:3(n − 3), suggested that Ulva pertusa (Chlorophyta) seaweed bed supplied important food sources to intertidal bivalves. Additionally, result of stable isotope analysis showed that phytoplankton contributed 86.2 to 89.0% to intertidal bivalves’ carbon budget; macroalga U. pertusa origin source had a contribution of 8.7% to 11.0%, which indicated its role as an important supplemental food source to intertidal bivalves. From this study, it is concluded that the dietary difference of three bivalves probably relates to the different potential food sources in the scallop farm and intertidal zone in Jiaozhou Bay.