Freshwater fishes in India are poorly known and plagued by many unresolved cryptic species complexes that
masks some latent and endemic species. Limitations in traditional taxonomy have resulted in this crypticism.
Hence,molecular approaches like DNA barcoding, are needed to diagnose these latent species. Wehave analyzed
1383 barcode sequences of 175 Indian freshwater fish species available in the databases, ofwhich 172 sequences
of 70 specieswere generated. The congeneric and conspecific genetic divergenceswere calculated using Kimura's
2 parameter distance model followed by the construction of a Neighbor Joining tree using the MEGA 5.1. DNA
barcoding principle at its first hand approach, led to the straightforward identification of 82% of the studied species
with 2.9% (S.E = 0.2) divergence between the nearest congeners. However, after validating some cases of
synonymy and mislabeled sequences, 5% more species were found to be valid. Sequences submitted to the database
under different names were found to represent single species. On the other hand, some sequences of the
species like Barilius barna, Barilius bendelisis and Labeo bata were submitted to the database under a single
name but were found to represent either some unexplored species or latent species. Overall, 87% of the available
Indian freshwater fish barcodeswere diagnosed as true species in parity with the existing checklist and can act as
reference barcode for the particular taxa. For the remaining 13% (21 species) the correct species name was difficult
to assign as they depicted some erroneous identification and cryptic species complex. Thus, these barcodes
will need further assay and inclusion of barcodes of more specimens from same and sister species.