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Not AvailableIndian has a rich aquatic biodiversity spreading across different ecosystems. Total 2358 endemic fish species have been reported from India comprising marine (1368), brackish water (113) and freshwater fishes (877). Marine fish identification is seldom difficult because of their high diversity and profound changes in appearance during their development stages. DNA bar coding technique has been successfully used to discriminate all animal taxa. In this study, DNA barcodes were generated for 32 species representing 13 families of the order perciformes. The average genetic divergence values for within species, genus and family were 0.42, 13.91 and 18.05%, respectively. The genetic divergence values increased several folds (15-20 times) from lower to higher taxa. barcode gap analysis showed the absence of overlapping between intra and inter specific divergence values. Intraspecific variation has increased several folds (15-20 times) after including conspecific sequences from different geographical locations. Presence of allopatric lineages / cryptic species was observed in several fishes that have Indo-pacific region distribution. The neighbour joining (NJ) tree constructed based on mitochondrial cytochrome oxidase submit 1 Kimura two parameter (COL K2P) values showed distinct clusters shared by congeneric species. Around 100 nucleotide diagnostic character exclusive to Perciformes fish species were also identified.Not Availabl