Abstract: The Bryde’s whale is a medium sized baleen whale that is widely distributed in the tropical and subtropical waters. However, the taxonomy of the Bryde’s whale has long been controversial. Currently, both the IUCN (the International Union for Conservation of Nature and Natural Resources), and the IWC (the International Whaling Commission) assign the whale as two subspecies, Balaenoptera edeni edeni and B. e. brydei. Although, several studies indicate that they should be regarded as two separate species, B. e. edeni and B. e. brydei are so similar in their external morphology, and are sometimes sympatric, which make it is difficult to correctly identify them in the field just through observation. Therefore, accurate species delimitation usually requires molecular methods. Recently, a Bryde’s whale population was reported inhabiting in the Weizhou Island waters, Beibu Gulf. However, it is unclear which species these animals belong to. In this study, we collected two fecal samples from two individuals in this population, and tried to identify them using molecular methods. Genomic DNA was extracted from one of the two fecal samples. Fragments of the mitochondrial genes Cyt b and COⅠ were PCR amplified and sequenced. Based on the mitochondrial gene sequences, the whale was identified as B. e. edeni. In addition, a baleen whale that died in 2019 in the same waters was also identified as B. e. edeni using the same methods outline in this study. Thus, we infer that the population living in the Weizhou Island waters is B. e. edeni. This is the first study which successfully identified a living Bryde’s whale based on mitochondrial DNA present in fecal samples. This non-invasive sampling-based species identification method should be further developed and applied in the future. Additional studies, such as population genetics should be carried out to provide a scientific basis for the conservation of this Bryde’s whale population.