Population biology, which has been mainly studing the terrestrial animals and plants, is an important branch of ecology. During these years, there are some researches extending to the hydrobiont populations, such as fish and shrimp populations and get many interesting results. However, because of the ambiguity of the definition of micro-hydrobiological populations and some hypotheses hold that all individuals of species in a lake belong to one population and free living species are cosmopolitan, the researches in this area lagged behind that of terrestrial populations; the studies of micro-hydrobiological population are rare in literature. In this research RAPD has been used to study the genetic diversity of Carchesium polypinum populations that have been sampled from three lakes that include Lake Donghu (D), Lake Nanhu (N) and Lake Shahu (S). The procured results have been used to deduce the definition of the C. polypinum populations.We used 120 arbitrary primers to amplify the DNA extracted from the five C. polypinum samples and from this 31 primers resulted in giving out positive bands.The result were as followed: (1) the 20 primers produced 172 clear bands with an average of 8.6 fragments, ranging from 100bp to 1600bp,. The other 11 primers produced 59 legible bands in an average of 5.4 fragments that ranged from 100bp to 1500bp; (2) Results of SPSS 12.0 and RAPDistance 1.04 that had similar trees were composed of two parallel main branches. Samples from Shijizhong (Z) of D, Shuiguohu (H) of D and N clustered into a branch and another sample from D-Fengguangcun(F) gathered with S or itself made another main branch. The result that the three samples of D were separated by the samples of other lakes suggested that the individuals of C. polypinum in D belong to several populations. This discovery will promote the population ecology researches of micro-hydrobiont, moreover, it will help study the essence of its transitional zone and the behavior of dispersal and vicaricance. This report can dedicate to the investigations of population differentiation and the mechanism of speciation.