Abstract: PCR-based DNA fingerprinting techniques such as random amplified polymorphic DNA analysis(RAPD)represents a very informative and cost-effective approach for assessing genetic diversity of a wide range of organisms. As a powerful molecular biology technology,DNA fingerprinting is widely applied on the study of integral genetic structure. All DNA fingerprinting techniques can discover the genetic diversity. For a individual or cell,they can discover the diversity of one genome; For population,they can discover the diversity of total DNA including many individuals. If for community, more information for different species can be discovered from many kinds of DNA templates. However,it is restricted to population and individual-level life system. This paper first explored the feasibility for application of DNA fingerprinting to community-level life system with plankton community from three stations of different eutrophic status in Lake Donghu as samples. Total community DNAs were extracted. PCR fingerprinting techniques based on the use of arbitrary primers(RAPD-PCR)have been developed and compared for their ability to generate“fingerprint”patterns characteristics. 20 RAPD primers were screened. 5 primers which amplified clear and sharp bands were used to discuss from these total RAPD primers. The results show that(1)we constructed a DNA extraction method adapating to plankton community through a series of getting rid of impurities. The high quality of template DNA is a precondition for DNA fingerprinting analysis. The composition and their concentration are key factors for DNA extraction. The template DNAs extracted from Station Ⅰ of hypertrophication,Station Ⅱ of eutrophication and Station Ⅲ of mesotrophication,respectively,were amplified repreduciblely;(2)the resulting amplified maps are clear and stable in both RAPD by random primers M-01,M-02,M-03,M-18 and M-19,and PCR by specific primers CW 15946/47,EGMS6,EGMS4,ITS1 and HSP,and there were some relationship between the topological structure and trophic status. From RAPD and specific primers PCR amplification, there are many variations among three stations. Station Ⅲ comprising 33%—100% bands of Station Ⅰ or Station Ⅱ. This indicats species biodiversity of Station Ⅲ is the highest. In addition,the DNA fingerprinting maps obtained were tentatively and qualitatively discussed with the available data of species biodiversity and physical chemistry. In the present work,the results of this study will contribute to our understanding of the feasibility for application of DNA fingerprinting to community-level life system in plankton.