The Malaysian fish production is about 1.5 million metric tonnes and 86.9% of this comes from the marine sector and 13.1% from the inland sector. This included fish production by capture and culture. (DOF, 2002). Fisheries genetic resources need to have a value in terms of economic, ecological and social uses and they need to characterized. This is the mandate to FAO and it is also necessary for fisheries management and aquaculture development. The vast aquatic diversity that exists in Malaysia consist of numerous taxa of marine and freshwater fishes, crustaceans, mollusks, plants and animals. These figures could be an underestimate to the actual figure. The levels of genetic diversity includes ecosystems, communities, population, genotypes and individual genes. A knowledge of the genetic background of a species and its population structure is essential for its management, breeding and conservation programmes in fisheries. Problems like how to choose the right candidates for breeding, identifiying and monitoring lines, families and individuals, monitoring and control of inbreeding, inheritance of simple traits and genetic improvement through selection for favourable gene and gene combinations can potentially be answered through the use of molecular markers in the management of fisheries genetic resources.