Abstract: Amid comprehensive fishing bans and the continuous advancement of major infrastructure projects, the implementation of Technical Guidelines for Ecological Impact Assessment (HJ 19-2022) faces three contradictions: restrictions on traditional survey methods, insufficient efficiency in large-scale ecological assessment, and lack of historical data. Environmental DNA (eDNA) technology, with the advantages of high sensitivity, non-invasiveness and high-throughput capabilities, offers a new pathway to resolve these dilemmas. We systematically analyzed the unique value of eDNA in addressing the core contradictions in ecological impact assessment (EIA), and proposed a three-level collaborative implementation framework - “screening-locking, verification-qualification, monitoring-tracking”. Drawing on the environmental impact assessments of the Fuling to Fengdu Waterway Regulation Project on the Upper Yangtze River and the tender announcement of the Yangzhong Reach Phase Ⅱ (Emergency Regulation) Project, we embedded eDNA technology into the entire EIA process. It critically addressed the bottlenecks in three aspects: the standardization of full-process eDNA workflows, the completeness of native aquatic organism reference gene databases, and the development of quantitative models linking eDNA concentration to biomass. Accordingly, an institutional integration support system was constructed, centered on a national technical specification for eDNA monitoring in aquatic ecological surveys and whole-process quality control, underpinned by a national aquatic eDNA barcode reference database and independent third-party data quality verification. Through an eDNA dynamic monitoring network, the dynamic optimization of ecological conservation redlines and the precision of ecological-environmental access lists could be promoted, thereby achieving a strategic shift from “static delineation” to “dynamic monitoring” and from “passive assessment” to “proactive early warning”. Systematically integrating eDNA techno-logy into the environmental impact assessment system would be a crucial pathway to enhance ecological governance capabilities.

Key words: environmental DNA (eDNA), institutional integration, Three Lines and One Permit, EIA pathway, three-level collaboration