Correct identification is at the core of taxonomy. Although morphometric characterization is the most straightforward and cost-effective method, it has a number of limitations. By overcoming this limitation, bar coding of mitochondrial cytochrome c oxidase gene (COI) helps in accurate and cost-effective identification of fish species. This communication discusses limitations of conventional morphometry and how its integration with bar coding can help to solve the taxonomic ambiguity of morphologically similar species. Along with that information, different water bodies from J&K region have been analysed with special reference to fish diversity which revealed that the diversity is more in Jammu region as compared to Kashmir, due to favourable climatic conditions and larger number of lotic water bodies and also the fact that the integrated approach has been successfully adopted in Kashmir valley,contributing to accurate identification of fish fauna. There is a lot of room for research in this area as bar coding of fishes has just become popular in the Jammu region, despite its immaturity. This will aid in a better knowledge of the region's fish ecology, the preservation of the gene pool, and the rise of economically significant species.