Abstract: 【Objective】 To assess the phytoplankton biointegrity in typical sections of the lower reaches of Yangtze River based on environmental DNA （eDNA） technology,which could provide theoretical basis for evaluating the ecological restoration effects following the implementation of Yangtze River conservation initiative.【Method】 eDNA samples were collected during wet season （September 2021） and dry season （April 2021） from 3 typical sections of the lower reaches of Yangtze River:Anqing （AQ）,Wuhu （EH） and Jingjiang （JJ）.Reference and damaged points were selected in these 3 sections.Five candidate indicators were chosen by evaluating species richness,community species abundance,community structure composition and community trophic structure.A scoring system ranging from 0 to 5 was used to construct an evaluation system for phytoplankton biointegrity in typical sections of the lower reaches of Yangtze River. 【Result】 A total of 96 genera from 8 phyla of phytoplankton were identified in the 3 typical sections of Anqing,Wuhu and Jingjiang including Bacillariophyta,Chlorophyta,Cyanobacteria,Chrysophyta,Pyrrophyta,Phaeophyta,Rhodophyta,Haptophyta and Navicula,Rhizosolenia,Scenedesmus,Chroococcus,Microcystis,Volvox,Skeletonema.The total numbers of phytoplankton species in Anqing,Wuhu and Jingjiang sections at genus level were 4849,5746 and 7617 respectively in wet season,and decreased to 3933,4243 and 5683 respectively in dry season.During wet season,the dominant species in Anqing and Wuhu sections were Bacillariophyta,Cyanobacteria and Chlorophyta.In Jingjiang section,besides the dominant Bacillariophyta was the olominant.During dry season,the phytoplankton communities in all 3 sections were primarily composed of Bacillariophyta and Chlorophyta.In wet season,the scores for Anqing,Wuhu and Jingjiang sections were 17,16 and 15 respectively,with phytoplankton biointegrity grades of good,good and general.In dry season,the scores for Anqing,Wuhu and Jingjiang sections were 13,16 and 17 respectively,with phytoplankton biointegrity grades of genera,good and good.【Conclusion】 eDNA technology demonstrates high richness,high species diversity and detailed community composition in terms of species classification.It proves to be efficient and accurate in detecting phytoplankton species,plays a significant role in the selection of biological parameter indexes,and provides strong support for the construction of P-IBI evaluation system.