In recent years, polybrominated diphenyl ethers (PBDEs) are ubiquitous environmental contaminants, but its bioaccumulation and debromination in biota have remained largely unclear. In this study, we analyzed six PBDEs (BDE47, 99, 100, 153, 154, and 209) in various tissues (i.e., viscera, muscle, and gill) of 11 types of marine organisms including zooplankton, invertebrate and fish. The concentrations of six PBDE including BDE209 in marine organisms ranged from 0.75 to 7.29 ng/g dry weight, BDE209 from 0.46 to 6.78 ng/g dry weight, respectively. BDE209 was the dominant congener in all samples, followed by BDE47. The concentration ratio of BDE47, 99, 154 to ΣPBDEs in various tissues of organisms (i.e., Rapana venosa, shrimp, crab, cuttlefish, octopus, Synechogobius hasta, tonguefish and wolfish) increased, while the concentration ratio of BDE209 to ΣPBDEs decreased. Large differences of the concentration ratios between BDE99 and BDE100 in tissues of crab was found, ranging from 32:68 in crab viscera to 83:17 in crab leg muscle. Biomagnification factors for individual PBDE congeners ranged from 0.16 to 78.6. In general, the BMFs for BDE209 in muscle were higher than those in viscera within feeding relationships. The study results suggesting BDE209 can be biodegraded to BDE47 through BDE154 and BDE99 in marine organism, its metabolite importantly influenced by organism type not trophic level; higher percentage of BDE154 was found in viscera than that in other tissues in the analyzed marine organisms of Bohai Bay.