DNA barcoding has been advanced as a promising tool to aid species identification and discovery through the use of short, standardized gene targets. In the present study a species of crab, Liphyra perplexa was reported and was DNA barcoded for the first time in Indian waters. The study was carried out for identification of Lyphira perplexa (Crustacea, Brachyura, Leucosidae) present in Indian waters by DNA barcoding and by other conventional methods to understand the significance of its distribution. DNA sequence and morphologic data on crab species from marine habitat are summarized. Studies of distribution of any marine organism are very important to know the span of expansion in the oceans and to find out the factors behind that occurrence. In the present observation it describes the occurrence of the pebble crabs in Indian waters there by records a distributional area of the species from Indian waters. Nevertheless, barcoding remains one of the best methods to confirm species identification and mitochondrial COI data has an advantage over an individual dataset because of its high resolving power.