Research on the kinetics of Benzo[a]pyrene (B[a]P) bioaccumulation in the clam Pinctada martensii and mussel Perna viridis showed that the initial rate of uptake was directly related to the PAH concentrations in the ambient environment. The uptake and depuration rate constants were different at the four B[a]P exposure levels, which indicated that the toxicokinetic rate constants mainly depended on the exposure levels of pollutants to the environment. In addition, the uptake rate constants of B[a]P were higher than the depuration rate constants in the entire experiment. The comparison demonstrated that mussels release B[a]P more rapidly than clams. The bioconcentration factors (BCFs) of B[a]P varied from 3335 to 12892 in the clam and 2373–6235 in the mussel. These findings on the bioaccumulation kinetics for petroleum hydrocarbons, in association with the critical body residue, will be valuable when choosing sensitive organisms to assess the potential ecotoxicological risk to the marine environment.