Effective conservation relies both on the presence of a community with strong sense of management and accurate biodiversity information. Environmental DNA (eDNA) has been increasingly used as a biodiversity assessment tool that can provide fast and accurate data. Iriomote Island is a UNESCO World Heritage Site due to its unique biodiversity. While 90% of the island is protected as a National Park, no regular fish census and monitoring have been conducted. eDNA metabarcoding was used to identify fish biodiversity and distribution in Nakama River, largest mangrove habitat in Japan. Water samples were collected in December 2023 and April 2024, wherein a total of 240 fish OTUs in which 151 fish species, 115 genera and 53 family were annotated, including 5 critically endangered species from the Japan RedList, 15 additional species of conservation interest, and one invasive species were detected. Both samples showed similar fish community composition that are strongly correlated with vegetation type and salinity. Highest species richness was observed at mid-river mangrove dominated estuarine sites. The study is successful in providing baseline data on fish biodiversity using eDNA metabarcoding and further reinforcing the need to improve the conservation and protection measures for the mangroves of Nakama River.
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