Groupers are coral reefs associated and favored in the aquaculture industry. Aquaculture system has been successfully carried out with a floating cage system as well as in an aquaculture system in a pond. Lately, breeding activities in groupers have produced hybrid species that are expected to increase production and fulfillment of the demand of groupers in the live fish market in Singapore, Taiwan, and China. The study of biology has supported the success of many of groupers, but information on genetic variation in commercial groupers is still very limited. This report is a preliminary study of genetic diversity in commercial groups from Java, Bali, and Aceh, which is the Sunda land region in western Indonesia. Eleven specimens have been identified with the barcode region (Cytochrome c Oxidase subunit I gene region). As a result, two species were identified as Indonesian haplotypes, namely Epinephelus merra and Cephalopholis cyanostigma. Phylogenetic tree analysis produces two large clades, namely Clade I (Epinephelus) and Clade II (Cephalopholis and Variola), which are clearly separated in the subfamily Epinephelinae. However, in-depth studies of genetic variation need to be more accurate by increasing the number of specimens from various regions in Indonesia to describe genetic diversity comprehensively.