Molecular techniques provide powerful tools that enable accurate identification of most animal species. We amplify mitochondrial DNA fragments recovered from 29 bone samples putatively attributed to cetaceans using a touch-down and nested PCR procedure, then identify species on the basis of a BLAST GenBank search of reference sequences and a neighbor-joining tree implemented in DNA Surveillance. Mitochondrial DNA successfully amplified from 93.1% of these bone samples is used to identify four Mysticeti and five Odontoceti cetacean species, including one, the fin whale Balaenoptera physalus, that is for the first time reported from this region. Touch-down and nested PCR procedures greatly increase the rate of successful molecular identification of species from bone samples. Using these techniques, and applying them to hitherto unidentified bone samples, we demonstrate the value of this technology for improving our understanding of cetacean species diversity and composition along the western coast of the Taiwan Strait, China.