Recently, molecular ecology has been appearing to increasing attention, many kinds of molecular methods were applied in this field.In addition, various experts have been interesting in the Three-Gorges Reservoir region (TGRR) and even the whole Yangtze drainage basin after the beginning of dam engineering.However, few studies were focused on the molecular ecology of TGRR.In order to explore the relationship between genetic diversity and species diversity, the whole DNA of plankton communities from seven samples locations in the TGRR was analyzed by random amplified polymorphic DNA (RAPD), and species of which were identified as well.The 7 locations can be clustered into 3 groups by genetic diversity.Station A, C, D and E cluster as one group, station B and F cluster as another group, and station G is different from all of others.While these stations still as a whole after analyzing by RAPDistancel.04.Also, 41 species were found in all, which contains 4 algae, 10 protozoa, 19 rotifer, 4 cladocera and copepoda respectively.Meanwhile, the nearest genetic distance is only 0.2586 which occurred between station D and C, and the opposite one lies between D and F which is 0.4758.But species diversity analysis displays that station B and C have the nearest distance;correspondingly, A and F have the furthest one.In other words, the result of genetic diversity is not consistent with that of species diversity.Therefore, more information has been obtained from genetic diversity in river, which applied new information for establishing the relationship between genetic diversity and species diversity of plankton.And more molecular biological methods should be applied, such as that more sensitive as well as good replied approaches could analyze pronucleus and eukaryon re-spectively.