An attempt has been made in the present study in which partial sequencing of COI gene was carried out for the Scylla olivacea of genus Scylla, collected from Pichavaram mangroves of southeast India. The phylogenetic tree created using Minimum Evolution (ME), Maximum Likelihood (ML) and Neighbor - Joining (NJ) approaches proved that all the three methods produced same topology. The overall average genetic distance is 0.093. The mitochondrial sequence (Cytochrome oxidase subunit I) obtained from the specimen was the first sequence deposition at GenBank from Indian waters. The present study on partial COI sequencing (Barcoding) resolved the taxonomic ambiguity among the members of the genus Scylla to a greater extent.