Tilak R. ShresthaPoudel, Pradip2026-04-242026-04-242016https://hdl.handle.net/20.500.14540/26414Approximately 650-bp sequences of mitochondrial DNA (mtDNA) have been designated as ‘‘DNA barcodes’’ and have become one of the most contentious and animated issues in the application of genetic information to global biodiversity assessment and species identification. Mitochondrial COI region has become well established marker for animal DNA barcoding. However, we suggest that the utility of barcodes is suspect and vulnerable to technical challenges that are particularly pertinent to mtDNA. The region possess high Taxonomic conservation as well as enough Variability for species discrimination. Although the Barcode Library for all organism present in the Earth Primarily aimed at Facilitating identification, its application in forensic science, identification of mislabeling, ecological studies, food web study, phylogenetic study and population genetics has been proved by ongoing intensive studies. Nepal is rich in Biodiversity with abundant endemic flora and fauna, this type of research will be a milestone in the genetically diverse country like Nepal. Overexploitation of freshwater ecosystem possess serious threat to fish and fisheries DNA barcoding aid the accurate estimation of Biodiversity and its conservation. Keywords: DNA Barcoding, COI-5P, K2P model, transition/transversionsubstitution, Phylogeneticen-USBiodiversityPhylogeneticThesis