Application of molecular tools for the identification of threatened marine mammals has gained importance in recent years. Though live and dead strandings of cetaceans are common along the Indian coasts, the specimens are often not properly identified due to the lack of local taxonomic expertise and poor quality of the specimens. Two marine mammals washed ashore in a putrefied condition at Edayar (08°25′N lat., 76°57′E long.), Thiruvananthapuram District, southwest coast of India, were identified by sequencing of 16S rRNA and COI genes. Sequence and phylogenetic similarity search done with all entries in the DNA sequence database, GenBank using BLAST identified the stranded mammals as Bryde’s whale (Balaenoptera edeni) and finless porpoise (Neophocaena phocaenoides). The present report is the second record of B. edeni from the southwest coast of India.