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The most economically important form of aquaculture is fish farming, which is an industry that accounts for an ever increasing share of world fishery production. Molecular markers can be used to enhance the productivity of the aquaculture and fish industries to meet the increasing demand. Molecular markers can be identified via a DNA test regardless of the developmental stage, age or environmental challenges experienced by the organism. The application of 16s and cytochrome b markers has enabled rapid progress in investigations of genetic variability and inbreeding, parentage assignments, species and strain identification and the construction of high resolution genetic linkage maps for aquaculture fisheries. In this review, the advantages of principles and potential power tools of 16s and cytochrome b markers are discussed. Main findings in term of trend, aspects and debates on the reviewed issue made from the model of aquatic species for the benefit of aquaculture genomics and aquaculture genetics research are discussed. The concepts in this review are illustrated with various research examples and results that relate theory to reality and provide a strong review of the current status of these biotechnology topics.

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Abstract-Molecular markers can be identified via a DNA test regardless of the developmental stage, age, or environmental challenges experienced by the organism. The degree of conservation of sequence using the cytochrome b gene from mitochondrial DNA is sufficient to discriminate between closely related species. A partial DNA sequence of cytochrome b gene was used to investigate the molecular relationship between Epinephelus hexagonatus and Epinephelus fuscoguttatus. Polymerase Chain Reaction (PCR) and sequence analysis were used to determine the genetic variation in approximately 450-nucleotides region of the mitochondrial cytochrome b gene in 160 fresh tissue samples. Phylogenetic trees were constructed using bioinformatic tools with ME method, NJ method and MP method with bootstrapping using arithmetic average method. There are no differences or only small differences were detected between these two taxa. The results showed that Epinephelus fuscoguttatus clustered with Epinephelus hexagonatus, based on the phylogenetic trees Epinephelus hexagonatus and Epinephelus fuscoguttatus consistently clustered together with following the suggestion referring on their morphological data, that they may be closely related, or possibly placed within the same species.