It is difficult to morphologically identify large whale carcasses because they were highly decomposed or damaged. In November 2018 and January 2019, two dead decomposed baleen whales were found respectively in Nantong, Jiangsu Province and Ningbo, Zhejiang Province. Their morphological features were checked, and molecular biology technique was used, 903 bp and 972 bp of mtDNA control region sequences as well as 467 bp and 438 bp of Cyt b sequences were obtained, respectively. After GenBank alignment, the samples from Nantong and Ningbo had the 99%-100% and 97%-99% similarity respectively and with the Fin whale (Balaenoptera physalus) and the Omura’s whale (B. omurai). The phylogenetic tree constructed by the maximum likelihood method in MEGA 7.0 software was consistent with the GeneBank alignment results. Based on two methods, the baleen whales in Nantong and Ningbo were respectively identified as Fin whale and Omura’s whale. The study confirmed the new distribution information of Fin whales in Nantong, Jiangsu Province and Omura’s whale in Xiangshan, Ningbo, Zhejiang Province.