A pilot study of fish biodiversity with a highlight of chondrichthyans in Hong Kong waters using environmental DNA metabarcoding

Assessing marine fish biodiversity, particularly high trophic level and conservation value species like chondrichthyans (sharks, rays, and skates), is crucial for evaluating the health of local fisheries and the sustainability of coastal ecosystems. Hong Kong boasts a diverse coastal ecosystem and harbors a wide variety of marine fish species. Yet traditional fish survey methods often fall short of efficiently assessing local fish diversity. In this study, we employed the non-invasive environmental DNA (eDNA) method, to evaluate the overall fish diversity in Hong Kong, with a focus on chondrichthyans. We collected full-depth water samples from the eastern, southern, and western waters of Hong Kong. The primer set Elas12S was used to target chondrichthyans, while 12S_V5 was used to screen for all fish species. We successfully detected five chondrichthyan species (Scoliodon laticaudus, Scoliodon macrorhynchos, Gymnura japonica, Telatrygon zugei, and Hemitrygon bennettii), two of which are Near Threatened and two are Vulnerable according to the IUCN Red List. The eDNA data unveiled 136 fish species from 54 families within Hong Kong's coastal waters, with Mugil cephalus exhibiting the highest level of abundance. The indicator species utilized to assess environmental conditions differed substantially across distinct hydrographic zones. Our findings in this eDNA pilot study conducted in Hong Kong demonstrate that the eDNA method can be applied to detect targeted, vulnerable or near-threatened fish species, such as sharks and rays. Furthermore, this rapid detection methodology could have valuable applications for long-term biodiversity monitoring and marine conservation. To enhance the eDNA method and its accuracy in species identification, we recommend establishing a comprehensive reference database of DNA barcodes for local fish species and investigating appropriate sampling efforts in the highly diverse waters of Hong Kong. © 2025 The Authors.