Arctic and Antarctic marine ecosystems, which are important components of global biodiversity, have been severely threatened by environmental pollutants in recent decades. In this study, polybrominated diphenyl ethers (PBDEs) and their hydroxylated and methoxylated analogues (OH-PBDEs and MeO-PBDEs) were analyzed in seawater, sediment, and marine organisms (algae, invertebrates, and fishes) collected surrounding the Arctic Yellow River Station (n = 83) and the Antarctic Great Wall Station (n = 72). PBDEs and the analogues were detectable in all polar marine matrices, except MeO-PBDEs in seawater. The concentrations of ∑PBDEs, ∑MeO-PBDEs, and ∑OH-PBDEs in the marine organisms were in the range of 0.33-16 ng/g lipid weight (lw), n.d.-2.6 ng/g lw, and 0.12-2.3 ng/g lw in the Arctic and 0.06-31 ng/g lw, n.d.-5.8 ng/g lw, and 0.17-35 ng/g lw in Antarctica, respectively. Biota-sediment bioaccumulation factor (BSAF, g TOC/g lipid) values of MeO-PBDEs (0.002-0.14) and OH-PBDEs (0.004-0.18) were lower than the BSAF values of PBDEs (0.85-12). Trophic magnification was found for ∑MeO-PBDEs, whereas trophic dilution was observed for ∑OH-PBDEs in both regions. This is one of very few investigations on trophic transfer of PBDE metabolites in the Antarctic and Arctic regions and will further strengthen concerns about the ecological risk of PBDE metabolites in remote areas.