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The increasing discharge and ubiquitous occurrence of novel brominated flame retardants (NBFRs) in aquatic environments have initiated intense global concerns; however, little information is available regarding their structure-related trophodynamics in marine food webs. In this study, a tropical marine food web including 29 species (18 fish and 11 invertebrate species) was collected from coral reef waters of the Xisha Islands, the South China Sea, for an analysis of 11 representative NBFRs. The mean ∑NBFR concentrations generally increased in the following sequence: sea cucumbers (0.330 ng/g lw) < crabs (0.380 ng/g lw) < shells (2.10 ng/g lw) < herbivorous fishes (2.30 ng/g lw) < carnivorous fishes (4.13 ng/g lw), with decabromodiphenyl ethane (DBDPE) and hexabromobenzene (HBB) as the predominant components. Trophic magnification was observed for all of the investigated NBFRs, with trophic magnification factors (TMFs) ranging from 1.53 (tetrabromobisphenol A bis­(dibromopropyl ether)) to 5.32 (HBB). Significant negative correlations were also found between the TMFs and the tested in vitro transformation clearance rates (CL in vitro ) for the target NBFRs except for bis­(2-ethylhexyl)-3,4,5,6-tetrabromo-phthalate (TBPH) (p < 0.05). Multiple linear regression analysis confirmed that the transformation rate is a more powerful predictor for TMFs than the hydrophobicity of NBFRs in this marine food web.