The Giant Grouper (Epinephelus lanceolatus), Mouse Grouper (Cromileptes altivelis) and the Brown Marbled Grouper (Epinephelus fuscoguttatus) are all found in the coastal waters of Sabah, Malaysia; they are listed as vulnerable, threatened and near-threatened, respectively, according to the IUCN Red Data list. Based on microsatellite loci, molecular markers can be applied as versatile tools for forensic detection, population genetic studies and the development of genomic databases which can subsequently be incorporated into viable conservation programmes. This paper describes the development of molecular markers for the three species of grouper. DNA was extracted from adult specimens of the three species, which are currently maintained at the Borneo Marine Research Institute Aquaculture facility, subject to DNA amplification using a multiplex PCR enrichment procedure, and the PCR products were ligated onto a pJET 1.2 blunt cloning vector. This was followed by sequencing and the development of 24 specific molecular markers for each of the three species. These markers have a potential application for the identification and forensic detection of these species in transit and can be adopted within the context of a strategy for the conservation and management of Malaysian fisheries resources.