The rapidly growing aquaculture industry with an estimated value of over US$51 billion contributes significantly to total global fisheries production. Malaysia ranks fourth in Grouper production globally and there exists a significant potential for the development of this important fishery resource, considering the fact that the maritime territorial waters of Malaysia host a range of genetically diverse Grouper species. One of the major bottlenecks associated with the development of aquaculture in the country is the non-availability of high quality brood stock, with the requisite characteristics suited for aquaculture. In order to address this problem, the Borneo Marine Research Institute has developed four grouper hybrids based on four parental genotypes. The proposed study aims to characterise the four parental genotypes which are Epinephelus lanceolatis, Epinephelus coioides, Epinephelus fuscoguttatus and Cromileptes altivelis by constructing small insert genomic libraries for each species, followed by the elucidation of Mendelian inheritance patterns in the four hybrid genotypes developed using the four parental genotypes (Box 1.0). This will be the first study of its kind in Malaysia and will result in the development of approximately 400 to 600 molecular markers which will be deployed to characterise the population structure of the hybrid genotypes in terms of population genetic parameters such as allelic diversity, population structure cross-amplification of genomic loci, and the linkage of quantitative phenotypic traits to molecular markers. The results of this study will (i) facilitate the understanding of the process of genetic recombination in hybrids at a genomic level (ii) be of relevance to the selection of brood stock and juveniles with a high level of genetic fitness on the basis of data derived using molecular markers, and (iii) assist in the DNA fingerprinting and population diversity analysis of wild grouper populations. The data generated by the proposed study will have a significant impact on the fundamental understanding of the molecular genetic processes involved in the mechanism of hybridization and its effects on phenotypic characteristics (Box 2.0). The study will also facilitate the management of the brooder germplasm through the process of marker-assisted selection on the basis of genetic diversity, this will further translate into economic gains, as the fry selected for stocking will exhibit a higher growth rate and lower susceptibility to stress and diseases. In terms of achieving national food security, the study will provide Malaysian researchers with access to a database of molecular markers for application n current and future breeding programs.