In order to identify a decayed large body of Baleen whale, found at the converging area of Yangtze Estuary and Hangzhou Bay, three regions of mtDNA (control region, cytochrome c oxidase subunitⅠ, COⅠ and cytochrome b, Cyt b) were sequenced. The sequencing results showed that the control region was 976 bp (GenBank accession: MF781125), COⅠ was 642 bp (MG010134) and Cyt b was 307 bp (MG010133). UPGMA and ML gene trees of the control region based on HKG + G model of 17 Baleen whales suggested that the body was among individuals in branch of Balaenoptera physalus (Fig. 4 and Fig. 5). Only a C/T transition in the control region was found between decay body and two B. physalus samples (KC572816 and KC572776) from coastal zone of California, America. The COⅠ and Cyt b sequences contained several termination codons, and the blasting results in GenBank verified that sequences of high homology were not available. The results unequivocally identified the body as B. physalus and its geographical origin was the North Pacific. Moreover, COⅠ and Cyt b in the body could be nuclear mitochondrial pseudogenes.