Display omitted •Accurate subspecies identification of free-ranging whales can be achieved using noninvasive eDNA technology.•Various mtDNA markers in eDNA can be used for genetic identification of cetaceans and reconstruction of their phylogenies.•Eden’s whale might mainly fed on sardines and anchovies in Dapeng Bay, Guangdong Province, China.•eDNA technology is potentially useful as an early warning system for the presence of cetaceans. Environmental DNA (eDNA) sampling of water is a powerful method for comprehensive and noninvasive monitoring of aquatic animal species. However, there have been few reports of its application to cetacean species. On June 29, 2021, a whale (nicknamed Xiaobu) appeared in Dapeng Bay off Guangdong Province, China. We used eDNA technology to obtain information related to this whale (e.g., species identification and food resources) and to trace its possible origin. Fragments of four whale mitochondrial sequences (12S rDNA, 16S rDNA, cytochrome c oxidase subunit 1, and control region) were obtained from amplicons of eDNA collected in Dapeng Bay; sequence barcoding showed that this was an Eden’s whale (Balaenoptera edeni edeni Anderson 1879). Analysis of potential prey species (PPS) suggested that this whale might enter Dapeng Bay while tracking prey, mainly sardines (Sardinella lemuru, Sardinella gibbosa and Sardinella jussieui) and anchovies (Thryssa dussumieri, Thryssa vitrirostris and Thryssa kammalensis). Retrieval of eDNA metabarcoding data from samples collected in waters adjacent to Dapeng Bay (i.e. Lingding Bay and Daya Bay) revealed that Eden’s whale had appeared outside Lingding Bay up to 2 months prior to the appearance of this whale in Dapeng Bay (early April 2021). Overall, this study showed that eDNA is a highly effective noninvasive survey method for the accurate identification of target cetacean species and prey composition; it can be used to monitor megafauna that are under strict legal protection or to monitor megafauna with unknown conditions.