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 focus for ecological study.In order to offer facilities and accumulate basic data for water quality assessment, this paper studied the relationship between genetic information of plankton community and the major environmental factors. The physico-chemical factors of seven sampling stations in Eastern Dongting Lake were measured with general methods and the DNA polymorphism of plankton community was analyzed by random amplified polymorphic DNA (RAPD). Then, their relationship was assessed with cluster analysis. The results were: (1) 11 of 80 screened random primers used in the study generated a total of 148 observable RAPD bands and 98.6% of which were polymorphic hands; the mumber of amplified bands at different sampling stations ranges from 45 to 70, the mean number was 57.6 and the station IV got the minimum; (2) the content of silt at station IV was the highest (75. 5 mg/L) and the other stations were from 1.2 to 40.3 mg/L; the discrepancy of other five factors measured in the investigation were not obvious in different stations. Cluster analysis based on RAPD markers and the major environmental factor showed that DNA fingerprinting of plankton community was correspondent to the content of silt. And the seven sampling stations could be grouped into two clusters : the station IV was a single cluster and another cluster consists of the other six stations.In conclusion, the DNA fingerprinting of plankton community was closely related to the environmental physico-chemical factors that mainly restrict the distribution of planktoric organisms, and the data of such kind accumulated will play an important role in constructing one handy and effectual system for water quality assessment.