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Planktonic larvae were captured in the shallow Vellar estuary, Tamilnadu, India, during January to June 2013 using zooplankton net. Larvae were identified to the species level by comparison with Genbank data base using MtDNA sequence data. Further analysis showed that there is no sequence variation within-species, whereas between-species variation was more than 25%, supporting the suitability for species identification. The highest genetic distance was observed between <i>A. nigropunctatus </i>and <i>M. cephalus </i>(0.434) and the lowest genetic distance was observed between <i>T. jarbua </i>and <i>S. commersoni </i>(0.256). </span><span lang="EN-IN" style="font-size: 10.0pt; letter-spacing: -.2pt">Given the current worldwide interest in DNA barcoding and species identification using MtDNA gene marker (CO1), it was confirmed the efficacy of the Fish-F1 and -R1 primer set, which gave the possibility for identification of finfish larvae at species level.