The green-lipped mussel Perna viridis’ sensitive nature and characteristic as a benthos organism that filters the sediment in its environment make it one of the possible bioindicators for pollution in the aquatic ecosystem. The present study aimed to determine the percentages of total shell deformities in comparison to the past data in the coastal waters of Peninsular Malaysia. It was found that several types of discontinuous, continuous, and unexplained shell abnormalities contributed to the overall range of shell deformities of 15.8–87.5%, which was greater in comparison to that (0.0–36.8%). The present study showed that the highest overall proportion of shell abnormalities occurred in Teluk Jawa, whereas the lowest percentages were found in Kampung (Kg.) Pasir Puteh. The regulative mechanisms at the well-known polluted sites at Kg. Pasir Puteh could be the explanation. Further research should be conducted to determine the degree of heavy metal that may be the source of these malformations in the mussel shells.