Random amplified polymorphic DNA( RAPD) markers were applied to analyze genetic relationships of Stentor coeruleus that were sampled from four water areas including Lake Donghu (D. Lake), Lake Nanhu (N. Lake), Lake Yuehu (Y. Lake) and Pond Guanqiao (G. Pond). Their Genomes were amplified with 12 random primers. Distinctly different banding patterns were obtained, with which the genetic relationship of organisms treated was deduced: the genetic distance among the sample was 0.076-0.416. The phylogenetic tree was constructed by Rapdistance 1.04. The results showed that three samples from N. Lake clustered into one branch which indicated S. coeruleus in the lake belong to one population, but 3 samples from D. Lake were separated by the sample from G. Pond which showed that S. coeruleus in it belong to different populations. This discovery supported the hypothesis of vicariance in geographic. It will promote the researches on the population ecology of micro-hydrobiont, and the development of phylogeography and vicariance biogeography.