In this study, the ranges of pollutants found in the soft tissues of Perna viridis collected from Kg. Masai and Kg. Sg. Melayu, both located in the Straits of Johore, were 0.85-1.58 μg/g dry weight (dw) for Cd, 5.52-12.2 μg/g dw for Cu, 5.66-8.93 μg/g dw for Ni and 63.4-72.3 μg/g dw for Zn, and 36.4-244 ng/g dry weight for ∑PAHs. Significantly (p < 0.05) higher concentrations of Cd, Cu, Ni, Zn and ∑PAHs in the mussels were found in the water of a seaport site at Kg. Masai than a non-seaport site at Kg. Sg. Melayu population. The ratios of low molecular weight/high molecular weight hydrocarbons (2.94-3.42) and fluoranthene/pyrene (0.43-0.45) in mussels from both sites indicated the origin of the PAHs to be mainly petrogenic. This study has demonstrated the utility of using the soft tissues of P. viridis as a biomonitor of PAH contamination and bioavailability in the coastal waters of Peninsular Malaysia.