The Snakehead fishes have significant economic importance in Bangladesh as food due to their exquisite taste. Some species of snakeheads are considered in threatened categories due to their population decline and loss of habitats. DNA Barcoding has been considered as a global bio-identification system for freshwater and marine fishes in recent years. In the present study, four snakehead species: Channa gachua, C. marulius, C. punctata and C. striata were investigated using both morphological methods and molecular identification with mitochondrial Cytochrome c Oxidase subunit I (COI) gene. Our study confirms that no C. orientalis existing in Bangladesh and all the older reports are pertaining to C. gachua. Phylogenetic relationships, the divergence of sequences between species was determined using Kimura 2-parameter distance model, and a Maximum Likelihood tree was generated in which the COI sequences for each of the four species could clearly be discriminated. The average interspecies genetic divergence was 26.90%. The study strongly validated the efficacy of COI as an ideal marker for DNA barcoding of Bangladeshi freshwater fishes and identification of specific species that necessitate further taxonomic study