Abstract-Genetic markers have long been identified as diagnostic tools to monitor marine pollution, as marine organisms exhibit genetic polymorphisms as adaptation and response towards environmental contaminants. This study aimed to determine the relationship between the heavy metal levels and the genetic polymorphisms of N. lineata, which were collected from six different mangrove areas in Peninsular Malaysia. Inter-Simple Sequence Repeat (ISSR) markers were applied for genetic polymorphism study in the snails while heavy metal analysis was carried out by using the atomic absorption spectrophotometer (AAS) for Cd, Cu, Fe, Ni, Pb and Zn. The results showed that the clustering of genetic polymorphism was based on geographical influences while clustering of heavy metal levels was based on bioaccumulation of the metals by the snails. However, there were no relationship between clustering patterns of the genetic polymorphism and heavy metal levels of the snails. This indicated that the population genetic diversity of N. lineata is not a suitable biomarker for heavy metal.