Abstract: Cyclomorphosis of rotifer defines the temporal cyclic morphological changes that occur within a rotifer population, including variation in body size, presence or absence and lengths of lateral spines and posteriolateral spines. This widespread phenomenon has complicated rotifer taxonomy. The study on genetic differentiation among different rotifer morphotypes by using molecular markers can help us to recognize their taxonomical status correctly. In the pre-sent study, the ITS sequences of 30 (S1-S30) spined and 18 (U1-U18) unspined Brachionus calyciflorus clones, col-lected from Lake Liantang, were analyzed, and their molecular phylogenetic trees were constructed by Neighbor-Joining (NJ), Maximum-Parsimony (MP), Maximum-Likelihood (ML) and Bayesian methods using B. patulus as an outgroup. The results showed that all the 48 clones belonged to 16 haplotypes. Within ITS sequence, the average content of T, C, A and G base was 28.6%, 18.7%, 35.9% and 16.8%, respectively. The content of A base plus T base was 64.5%, but that of C base plus G base was 35.5%. The sequence divergence was 26.2%-26.6% between haplotype U12 and the other haplotypes, with an average of 26.47%. The sequence divergence occurred in ITS1, 5.8S and ITS2 was 26.9%-27.8%, 2.9%-3.5% and 44.4%-45.0%, and the mean value was 27.27%, 3.09% and 44.48%, respectively. However, the av-erage sequence divergence was 0.41% among the other haplotypes. All the four phylogenetic trees supported that 48 clones should be obviously divided into two different clades. The first clade included clone U12, and the second one included all the spined clones and the other unspined clones. Haplotype U12 and the other haplotypes belonged to two sibling species, but the two B. calyciflorus morphotypes were not different subspecies or sibling species, and their variation in morphology attributed mainly to phenotypic plasticity.