The current study measured the concentrations of 14 polybrominated diphenyl ethers (PBDEs) and eight methoxylated polybrominated diphenyl ethers (MeO-PBDEs) in a marine food web and estimated their trophic magnification factors (TMFs), to highlight the differences between invertebrates, fish, and seabirds. Concentrations of PBDEs were orders of magnitude greater in seabirds (184.07 AE 161.63 ng/g lipid wt) compared with invertebrates and fish (19.01 AE 14.14 ng/g lipid wt). Although the congener profiles in invertebrates, fish, and juvenile seabirds were dominated by BDE-47, the contributions of BDE-99 and BDE-153 in adult seabirds were also significant. Unlike PBDEs, however, higher average MeO-PBDE concentrations were detected in fish (126.27 AE 189.27 ng/g lipid wt) and bivalves (15.96 AE 11.82 ng/g lipid wt) than in seabirds (2.61 AE 2.87 ng/g lipid wt). Correlations between lipid-normalized PBDE concentrations and trophic levels confirmed that seven PBDE congeners were magnified in the invertebrate-fish-seabird food web and that PBDE concentrations increased at a much greater rate across trophic levels in seabirds than in invertebrates and fish. This result indicates that estimating TMFs of PBDEs separately for seabirds, invertebrates, and fish is preferable. For MeO-PBDEs, no significant relationships were obtained in the invertebrate-fish-seabird food web.