Abstract: Water resources are of great importance in maintaining the sustainable development of natural resources. However,with the rapid increase of population and economy, pollution leads to water crisis and other challenges on aquatic ecosystem.Therefore, how to assess water quality rapidly and accurately and maintain the health of aquatic ecosystem has become the focusfor ecological study.In order to offerfacilities and accumulate basic data for water quality assessment, this paper studied the relationship betweengenetic information of plankton community and the major environmental factors. The physico chemical factors of seven samplingstations in Eastern Dongting Lake were measured with general methods and the DNA polymorphism of plankton community wasanalyzed by random amplified polymorphic DNA (RAPD). Then,their relationship was assessed with cluster analysis. The resultswere: (1) 11of 80 screened random primers used in the study generated a total of 148 observable RAPD bands and 98.6 % ofwhich were polymorphic bands; the mumber of amplified bands at different sampling stations ranges from 45 to 70, the meannumber was 57.6 and the station Ⅳgot the minimum; (2) the content of silt at station Ⅳwas the highest (75.5 mg/L) and theother stations were from 1.2 to 40.3 mg/L ; the discrepancy of other five factors measured in the investigation were not obviousin different stations. Cluster analysis based on RAPD markers and the major environmental factor showed that DNAfingerprintingof plankton community was correspondent to the content of silt. And the seven sampling stations could be grouped into two clusters: the station Ⅳwas a single cluster and another cluster consists of the other six stations.In conclusion, the DNAfingerprintingof plankton community was closely related to the environmental physico chemical factors that mainly restrict the distribution of planktonc organisms, and the data of such kind accumulated will play an important rolein constructing one handy and effectual systemfor water quality assessment.