The genus Channa, commonly known as Snakeheads comprises a diverse variety of species that hold great significance in the commercial sectors. Their complexity and genetic variety show how adaptable they are to different environmental settings and shed light on their evolutionary history. To delve into the genetic intricacies of the genus Channa, we analyzed mitochondrial genetic diversity using 1372 COI sequences obtained from the Barcode of Life Data System (BOLD) database. The metadata and phylogenetic analysis revealed the presence of species complex within C. gachua and C. marulius, suggesting the potential existence of intra and inter-clades within one species group. Further, we selected four ecologically and economically important taxonomic groups to study their haplotype diversity and genetic differentiation. These species/taxonomic groups include C. striata, C. punctata, gachua species complex, and marulius species complex. The analysis indicated a substantial level of genetic differentiation and haplotype diversity in species groups indicating high gene flow within populations. Mitochondrial introgression and species complexes account for a significant section of errors in DNA barcodes, which are two of the primary challenges associated with employing DNA barcoding to identify species. Highlighting these challenges and ongoing uncertainties in specific taxonomic groups of genus Channa, the study argues that the efficacy of DNA barcoding and the genetic integrity of wild variation may be weakened when speciation results in the establishment of numerous cryptic taxa in a species complex.