Organic pollutants (PAHs, PCBs, and organochlorine pesticides (OCPs) from sediments and Asian green mussels (Perna viridis) in Jakarta Bay were studied using GC-MS/MS. The PAHs cocentrations in the sediments ranged from 186.64 to 915.71 µg.kg-1 per sediment dry weight (dw), while the PCBs and the OCPs concentrations ranged from 3 to 117 µg.kg-1 and 3 to 17.99 µg.kg-1 per sediment dw, respectively. For the P. viridis, 16 types of PAHs concentrations ranged from 591 to 997 µg.kg-1 per dw of mussels, while the OCPs concentrations varied from 5 to 6 µg.kg-1 per dw of mussel. The concentration of PAHs in mussels were higher than sediments, meanwhile the organic pollutant contains chlorine (PCBs and OCPs) were potentially found in sediments. The reclamation, urban and mangrove areas (station G and H) in this study found more highly risk of than other sampling stations of sediments and mussels. The According to the environmental risk assessment parameters (TEL, ERM, and ERL) from the sediment quality guidelines, the stations has various potential ecological risks, with Station G and H being most contaminated, while Station A being least polluted. Based on l'AFSSA (Agence Francaise de Securité Sanitaire des Aliments, 2003) P. viridis is shown to be highly contaminated in polluted stations (except station A) that were not recommended for consumption (> 200 µg.kg-1 tissue dw). The selected PAHs ratios, including Ant/∑178, Fl/∑202, BaAnt/∑228, and IPyr/∑276, potentially showed that the sources of the hydrocarbons in sediments were generally biogenic and terrigenous than for mussels were petroleum source.