Polybrominated diphenyl ethers (PBDEs) were analyzed in three invertebrate species, five fish species with different living and feeding habits, and surface sediments collected from the Pearl River Estuary, South China. The concentrations of 10 PBDE congeners (BDEs 28, 47, 66, 99, 100, 85, 154, 153, 138, and 183) ranged from 34.1 to 444.5 ng/g lipid and from 9.88 to 39.0 ng/g organic carbon in biota and sediment samples, respectively. In sediments and some biota samples, BDE 209 was found as the major congener, ranging from nondetectable to 623.5 ng/g lipid in biota samples and from 792 to 4,137 ng/g organic carbon in sediment samples. Different levels of PBDEs in various biota species were attributed to the different feeding habits of the aquatic species or their ability to metabolize PBDE. Different congener profiles between the biota and sediment samples were observed and attributed to the bioaccumulation potential or the ability to metabolize individual BDE congeners. Polybrominated diphenyl ether levels in the biota from the Pearl River Estuary correlated well with lipid contents but did not correlate with the biota lengths. The distribution of biota-sediment accumulation factors for individual PBDE congeners was consistent with the general pattern predicted from a widely used bioaccumulation model.