Stentor coeruleus is widely distributed in many regions of the world. In this paper, we selected five samples of Stentor coeruleus from three Lakes (Lake Nanhu, Lake Yuehu, Pond Guanqiao). Genotype data from these five samples were analyzed by Randomly Amplified Polymorphic DNA (RAPD) marker to assess the genetic diversity of the S. coeruleus populations. The results were as followed: (1) The 11 primers produced 89 clear bands with an average of 7.4 fragments, ranging from 100-1500bp. (2) Considerable genetic diversity in these populations was suggested using the calculating genetic distance (0.076-0.416) between them. (3)Assessment of differences in populations by the phylogenetic tree erected using Rapdistance 1.04 showed that the three samples from N. Lake clustered into one branch indicating that these samples belong to one biotype. Our results show that RAPD technology is a rapid, precise and sensitive technique for identification of S. coeruleus genotypes and provides experimental evidence for the applicability of RAPD on the genetic diversity of S. coeruleus. Moreover, it can help in investigations of differences in populations and the mechanism of speciation. However, the phylogenetic relationships within S. coeruleus, must be interpreted with caution.