Abstract: The western coast of Taiwan Strait in Fujian has abundant marine biomass and serves as a hotspot for cetacean diversity. Accurate taxonomic delineation of these endangered mammals is critical for their conservation, which is commonly dependent on carcass decomposition degree and observer expertise. To circumvent these limits, we constructed a regional DNA barcode reference database including mitochondrial COI and D-loop as markers for fifty-one stranded cetaceans collected along the Fujian coast between 2002 and 2020. Based on the morphological inspection and genetic verification, we successfully identified fourteen species belong to ten genera and six families, including a rarely reported Ziphiid species (Mesoplodon ginkgodens). Phylogenetic reconstruction and genetic distance analysis confirmed that application the COI and D-loop as species identification barcode for common cetaceans along the Fujian coast. The established barcode database not only refines the documented cetacean diversity in this region but also serves as a valuable supplementary tool for traditional morphological identification. This work further offers a primary foundation for long-term population monitoring and conservation management of marine mammals in the Taiwan Strait.