Abstract. Jefri E, Zamani EP, Subhan B, Madduppa HH. 2015. Molecular phylogeny inferred from mitochondrial DNA of the grouper Epinephelus spp. in Indonesia collected from local fish market. . Groupers are widely distributed in the tropical and subtropical coastal waters, and are globally one of the most commercially important groups of marine fish, commanding high market price and are being heavily targeted in fisheries. Over fishing in Indonesia becomes a pivotal factor, which is seriously threatening the grouper biodiversity, as separate catch statistics are not reported for most species, and landings are often summarized as 'serranids' or 'groupers'. This lack of species-specific catch data is due to the difficulty of identifying many of the species. The focus of this study was the tracking of molecular phylogeny of Epinephelus spp. of the family Serranidae. DNA amplification using mitochondrial cytochrome oxidase I resulted in 526-base pairs long sequences all samples. A total of seven species were characterized that are (Epinephelus areolatus, E. merra, E. fasciatus, E. longispinis, E. coioides, E. ongus and E. coeruleopunctatus). All of which were found to belong to 7 different clades in the constructed phylogenetic tree. E. ongus is genetically closest to E. coeruleopunctatus with genetic distance 0.091 (9%), whereas the farthest genetic distance was successfully identified between E. ongus and E. merra with genetic distance 0.178 (18%). Migration activity on spawning and movement of larvae that are affected by Indonesian Through flow suspected as the cause of the closeness between species grouper Epinephelus spp. in the phylogeny tree from several Indonesian seas, although information about the location and time of Epinephelus spp. spawning activity sometimes difficult to obtain certainty. Fish identification using molecular phylogenetic approach has been successfully applied in this study. It seems need further application on this method to avoid misidentification and due to high variety of species landing at local fish market. Nevertheless, this study would be an important data in the genetic management for the sustainable conservation and trade of grouper (Epinephelus spp.) in Indonesia.