Horizontal starch gel electrophoresis was used to estimate the levels of genetic variation for 8 different geographical populations (Penang, Pulau Aman, Bagan Lalang, Telok Emas, Sungai Muar, Tanjung Kupang, Pantai Lido, and Kampong Pasir Puteh) of the mussel, Perna viridis, collected from the waters off the west coast of Peninsular Malaysia. Fourteen polymorphic loci were observed. The observed mean heterozygosity ranged from 0.108 to 0.334, while the expected mean heterozygosity ranged from 0.133 to 0.301. The highest mean value for genetic distance (0.091) was found between the populations of Penang and Telok Emas while the lowest value (0.004) was found between those of Pantai Lido and Tanjung Kupang. The populations studied could be divided into 2 groups by the UPGMA dendrograrn based on Nei's (1978) genetic similarities. The groupings seemed to indicate differentiation into local populations. These results suggest that P viridis has a tendency to split into a number of geographical populations regardless of larval dispersal as a potential agent of gene flow. The mean F-ST value of 0.149 indicates that the mussel populations show a moderate degree of genetic differentiation. However, the mean genetic distance from the present study (0.048+/-0.004) falls within the range of genetic distances between conspecific populations of mussels (0.0-0.14). Therefore, the present study supports the use of the local mussel P viridis as a suitable biomonitoring agent for heavy metals. The range of genetic distance values (0.004-0.091) presented here can also serve as baseline data to which results of similar studies in the future can be compared to determine whether genetic divergence of mussel populations from the west coast of Peninsular Malaysia is taking place.