Reconstruction of phylogenetic relations among certain Serranidae fish could be applied to detect the biodiversity that is needed to conserve these biological resources. This study was designed to provide information about the molecular variations within and among numbers of economically important fishes (42 fish species that belong to three genera), using a simple and effective barcoding system. A comparative genetic analysis was carried out among some 16S r-RNA sequences in various Serranidae fish genera (Plectropomus, Cephalopholis and Epinephelus). Nucleotide composition, sequence conservation, single nucleotide polymorphism (SNP), haplotype diversity and nucleotide diversity were calculated in all these fish species. All of these fish samples were differentiated by the barcoding system. Average genetic distance values within Plectropomus, Epinephelus and Cephalopholis were 0.03, 0.039 and 0.048, respectively. Plectropomus species were found to be distantly related to both Epinephelus and Cephalopholis. The DNA barcoding system should be used in fisheries and aquaculture to conserve aquatic genetic resources.