Stereoisomers of 1,2,5,6,9,10-hexabromocyclododecane (HBCD) and 1,2-dibromo-4-(1,2-dibromoethyl)-cyclohexane (TBECH) were determined in sediments and 30 marine species in a marine food web to investigate their trophic transfer. Lipid content was found to affect the bioaccumulation of ΣHBCD and ΣTBECH in these species. Elevated biomagnification of each diastereomer from prey species to marine mammals was observed. For HBCD, biota samples showed a shift from γ- to α-HBCD when compared with sediments and technical mixtures; trophic magnification potential of (-)-α- and (+)-α-HBCD were observed in the food web, with trophic magnification factors (TMFs) of 11.8 and 8.7, respectively. For TBECH, the relative abundance of γ- and δ-TBECH exhibited an increasing trend from abiotic matrices to biota samples; trophic magnification was observed for each diastereomer, with TMFs ranging from 1.9 to 3.5. The enantioselective bioaccumulation of the first eluting enantiomer of δ-TBECH in organisms at higher TLs was consistently observed across samples. This is the first report on the trophic transfer of TBECH in the food web. The estimated daily intake of HBCD for Hong Kong residents was approximately 16-times higher than that for the general population in China, and the health risk to local children was high, based on the relevant available reference dose.