In order to identify an unknown whale vertebra’s species,genomic DNA is extracted from the bone powder by proteinase K and phenol/chloroform,and a partial Cyt b gene sequence as long as 565 bp is amplified by PCR(Polymerase Chain Reaction).The blasting result in GenBank shows that the vertebra sample has maximal similarity with Balaenoptera omurai,it is 99%.It indicates that the vertebra is Balaenoptera omurai.The phylogenetic tree based on UPGMA is consistent with the blasting result.Analysis of software MEGA shows that the Cyt b gene sequence of the vertebra sample has 1-2 nucleotides which are different from the homologous sequence of B.omurai(accession AB201257,AB201256),thus,the sequence is a new haplotype.This is the first record of B.omurai which distributes in the South China Sea.