Abstract—The present study determined concentrations of polybrominated diphenyl ethers (PBDEs) and hexabromocyclododecanes (HBCDs) in mussels, fish and surface sediments from Jakarta Bay and its surroundings, Indonesia to understand their levels and distribution in sediment and their bioaccumulation in biota. Concentrations of PBDEs and HBCDs in sediments varied widely depending on sampling locations, ranging from 0.15–130 ng/g dry wt. and <0.020–5.9 ng/g dry wt., respectively. Highest concentrations of both brominated flame retardants (BFRs) were found at the sampling locations near harbors, industrial and highly populated areas, implicating industrial and human activities as sources of these compounds to the environment. Calculation of mussel-to-sediment and fish-to-sediment ratios based on concentrations of BFRs in biota as lipid wt. basis and in sediment normalized to organic carbon, showed values>1 showing higher concentrations of certain PBDEs (BDE-28,-47,-99,-100,-153,-154) and α-HBCD in mussels and fishes than those in sediments. These results indicate that these compounds are highly transferrable and bioavailable to biota. However, BDE-209 and γ-HBCD (the dominant compounds in sediments) were not detected or occurred in lower concentrations in biota, indicating their low bioaccumulation potential and/or labile nature.