Malaysia's aquatic ecosystems contribute 1.6% of her gross domestic product and provide employment to about 100,000 people. They are sources of a significant proportion of the nation's food supply, mainly by marine capture fisheries; but aquaculture, both marine and freshwater is becoming increasingly important. Hence, characterization of the species diversity of Malaysian biological resources (bioresources) is of paramount importance. One of the key components in any biodiversity investigation is elucidation of the population genetic structure of the species being studied, as it is an indication of the status of the species within the ecosystem. It is here that biochemical protein level and molecular DNA level indicators play crucial roles. Thus far, the studies that had been done in Malaysia using such biochemical and molecular markers were mainly on freshwater aquatic species that are important to aquaculture such as the catfish, Mystus nemurus and Clarias macrocephalus, and tilapia, Oreochromis niloticus and O. mossambicus, and the prawns Penaeus monodon and P. merguiensis. Random Amplified Polymorphic DNA (RAPD) and microsatellite markers had been used to study two species of marine turtles that nest on Malaysia's pristine beaches, the hawk's bill turtle, Eretmochelys imbricata and the green turtle, Chelonia mydas. However, none of the top ten marine fish species endemic in this country had been studied yet. A start had been made to study the genetic structure of the green-lipped mussel, Perna viridis, with a view to using it as a biomonitoring agent of environmental pollution. An association was found between increased heterozygosity level for allozyme loci and heavy metal pollution index in this species. This paper discusses these findings and makes suggestions for the use of biochemical and molecular markers as potential biomonitoring agents of pollution levels in future ecotoxicological studies of Malaysia's aquatic ecosystems.

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