Abstract: Along with the development and progress of society economy,dams have been playing increasing important roles,and so does the Three-Gorges Dam.Inevitably,hydrobios,hydrochemistry and other key physico-chemical factors of water body were altered.In order to evaluate these changes,many pursuers study water quality through bio-detectors and physico-chemical factors.But both of the two methods failed to compare from different studies since different bio-detector and physico-chemical factors were adopted.In this paper,the author tries to probe into a new way through discussing the relationship between DNA structure of plankton community and physico-chemical factors in the Three-Gorges Reservoir region(TGRR).Random amplified polymorphic DNA(RAPD) was used to analyze DNA structure of plankton community,and got the result that 7 locations clustered into 3 groups.Station D and E clustered together at first,then A and C joined in this group;B and F was as another group,and G was different from all the others.While the physico-chemical factors clustering showed that station B and C clustered as a group at first,then adding D into this group;G and F clustered into another group;A and E was other two separated groups.After comparing,some stations such as A,C,D and E clustered close in RAPD while were away fram each other in physico-chemical factors.On the other hand,B-G and F-G clusteried apart from each other while reversed in physico-chemical factors analysis.All the results indicated two possibilities:One was that DNA structure of plankton community under RAPD analysis and physico-chemical factors analysis of water body in the TRGG correlate negatively;the other was because of the instantaneous samples,some natural and artificial factors,such as water flow,weather,man-made operations and so on,might affect the experiment results to some extent.Accordingly,new information about physico-chemical factors has been obtained,which is beneficial to affirm relationship of DNA structure of plankton community and physico-chemical factors.Further more,it is better for establishing a new assessment system of water quality.