Molecular taxonomy technique based on phylogenetic reconstruction of mitochondrial DNA (mtDNA) sequences developed by CMFRI was successfully applied to ratify species identity of one beach cast baleen whale, which was in fairly fresh condition and unambiguously identify another one, which had decayed beyond recognition. Genomic DNA was extracted from their skin tissues and the mtDNA PCR products were cycle sequenced and species identity was confirmed using a dedicated portal for cetaceans, Witness for Whales (www.dna-surveillance. auckland.ac.nz) containing sequences from specimens of whales, dolphins and porpoises identified by expert taxonomists and Blast search of NCBI (www.ncbi.nlm.nih.gov/). The sequences were deposited in the GenBank under accession numbers EF057442, EF057443 & EF057444. One of the whales, measuring about 20 m in total length, was stranded on 17th July 2006 in Kundugal near Mandapam (Gulf Mannar) and was identified as a male blue whale (Balaenoptera musculus). The other, measuring about 12m in total length was stranded in the same area on 8th August 2006 and identified this species as Bryde’s whale (Balaenoptera edeni). Application of PCR-based gender identification method developed by CMFRI determined the sex of B. edeni as male and also ratified sex determination of B. musculus based on external genitals
