Analysis of Fish Diversity and Invasive Species in the Cuijiang River Based on Environmental DNA Metabarcoding

eDNA metabarcoding provides distinct benefits—including non-invasiveness, cost-effectiveness, and high detection sensitivity—that make it particularly appropriate for aquatic ecosystem conservation and fisheries management. An environmental DNA (eDNA) metabarcoding survey was performed in the Cuijiang River to assess the feasibility of this technique for fish diversity monitoring. Fish diversity was evaluated through water collection, eDNA extraction and purification, and subsequent bioinformatics analysis. Our results revealed that the surveyed river section harbours at least 36 fish species, belonging to 30 genera, 13 families, and 6 orders. The fish community was numerically dominated by Cypriniformes. Notably, invasive alien species represented a relatively high proportion (24.72%) of the total operational taxonomic units (OTUs). Alpha diversity indices showed spatial heterogeneity among the monitoring sites, which is likely influenced by anthropogenic activities, land-use patterns, and hydrological connectivity in the sampling areas. Overall, eDNA metabarcoding proves to be an effective approach for fish diversity assessment and can serve as a valuable supplementary tool to conventional methods, with particular utility for the early detection of elusive and invasive species. We therefore recommend its incorporation into ongoing and future aquatic monitoring and conservation frameworks to strengthen early detection, habitat management, and biodiversity protection, thereby offering essential baseline data for future conservation and management of local fish diversity.