Coral trout Plectropomus loepardus is one of high economic value groupers throughout its geographical distribution, while it was listed as Near Threatened at 2004 IUCN Red List. Fisheries Research Institute, COA also developed the artificial propagation technology of P. leopardus recently. However, the information of biology and ecology of this fish is poorly researched and understood. Therefore, the aims of this project are to investigate and compare the genetic diversity and differentiation of P. leopardus (1) between different phenotypes (body color pattern), (2) among different sectors in Penghu (northern, inner and southern sectors) and (3) between wild and aquacultured stock inferred from mtDNA control region gene and microsatellite locus. According the above results, it could supply the reliable information for assessment and management of P. leopardus resource and help to genetic diversity monitor of aquacultured stock. Furthermore, it could develop the fingerprinting of microsatellite locus and help to screen the broodstock of P. leopardus which grow faster and have crimson body color.