Environmental DNA Metabarcoding Reveals Hidden Fish Diversity and Strong Habitat Partitioning Across Coastal Ecosystems in the Con Dao Archipelago, Vietnam

The Con Dao archipelago hosts the oldest MPA in Vietnam and is recognized as a regional marine biodiversity hotspot. Here, we applied environmental DNA (eDNA) metabarcoding to assess coastal fish diversity across four major habitat types: coral reefs, seagrass beds, mangroves, and a harbour in the Con Dao archipelago. Using MiFish-U 12S primers at eight stations, we detected 282 operational taxonomic units, corresponding to 144 fish taxa. Fish assemblages exhibited strong habitat structuring: community composition differed markedly among habitats, with minimal overlap. Only three species were shared across all habitats. Multivariate analyses confirmed that habitat type, rather than spatial distance among sites, was the primary driver of community differentiation. Mangrove and seagrass supported distinct assemblages that were underrepresented in existing species checklists and MPA management frameworks. Notably, eDNA detected cryptic and non-commercial species overlooked by conventional survey methods. These results substantially expand the known fish diversity of the Con Dao Archipelago and highlight the need to incorporate habitat heterogeneity, particularly non-reef ecosystems, into MPA design and monitoring. Although eDNA metabarcoding is subject to amplification biases and limited taxonomic resolution in reference databases, it offers a powerful complement to traditional surveys for characterizing under-sampled habitats.