Plankton are considered good indicators of water quality because they are highly sensitive to the environmental variation intheir short life spans. However, traditional studies on plankton community constructure have depended on taxonomic identificationwhich has historically been a difficult task. Recently, different fingerprinting techniques have been developed and appliedsuccessfully to analyze the community structure of bacterial and picoplankton. However, little is known to the whole planktoncommunity. In this study, we analyze DNA polymorphism of plankton communities in five different sampling stations of LakeNiushan by RAPD and PCR-DGGE and explore the relationship between DNA fingerprinting structure of plankton communities andenvironmental physico-chemical factors. The results were: (i) 9 of 40 screened random primers used in the study amplified a total of93 observable bands, 58 of which were polymorphic;the mean number of amplified bands at different sampling stations was 67, andstation Ⅴ had the maximum number (74) and station had Ⅰ the minimum number (61);(ii) a total of 102 bands (56 of 16S rDNAbands and 46 of 18S rDNA bands) were detected by PCR-DGGE, station,, and Ⅲ Ⅳ had more bands, Ⅴ station and Ⅰ had few Ⅱband;(iii) total phosphorus (TP), chlorophyll-a, chemical oxygen demanded (COD), hardness, and conductance rate at station wer Ⅱ ethe highest;dissolved oxygen (DO) and pH value were not obviously different among five stations. Based on physico-chemical factors,stationⅠ,, Ⅲ Ⅳ, and Ⅴ were grouped into a cluster, station Ⅱ grouped into a single cluster. Based on RAPD markers andPCR-DGGE markers, five sampling stations can be grouped into two clusters: stationⅠ and Ⅱ were grouped into a cluster, and station Ⅲ Ⅳ and Ⅴ were grouped into the other cluster. In conclusion, the DNA fingerprinting structure of plankton community wasclosely related to total phosphorus (TP). DNA based community level analysis is a fast, easy, accurate method to reflect the waterquality, and such data accumulation will play an important role in constructing one easy and sensitive molecular system for waterquality assessment.