The Indo-Pacific finless porpoise (Neophocaena phocaenoides), a coastal cetacean distributed from the Taiwan Strait to the Persian Gulf, is a critical sentinel of marine ecosystem health. Facing severe threats from fisheries bycatch and increasing strandings in Hong Kong, more efficient monitoring methods are required for this species beyond traditional surveys. Here, we employed environmental DNA (eDNA) analysis—a non-invasive, high-throughput approach—to detect this elusive porpoise in Hong Kong waters, focusing on the Soko Islands in the southern Hong Kong waters. In March 2025, we collected surface and bottom water samples across key habitats and applied both species-specific qPCR and eDNA metabarcoding using cetacean-specific primers. qPCR revealed spatial variability in eDNA concentrations, with higher levels in eastern waters near the Soko Islands. Metabarcoding not only detected the porpoise eDNA but also detected false killer whale (Pseudorca crassidens) eDNA, underscoring the method's potential for multi-species cetacean monitoring. While surface samples and qPCR showed marginally higher detection rates, no significant differences were found between water layers or methods. Our study validates eDNA as a powerful tool for monitoring finless porpoises and highlights the complementary value of combined two eDNA methods. These findings pave the way for applying eDNA to conserve elusive marine mammals in impacted coastal ecosystems.
 

Environmental DNA (eDNA),Coastal Cetacean,Metabarcoding,qPCR,Hong Kong Water