With the increasing seriousness of global warming and eutrophication, algal blooms occur frequently in freshwater lakes, and thus initiate ecotoxic effects of microcystins on aquatic organisms. In the present study, the combined effects of temperature (16, 20, 24 and 28℃) and microcystin MC-LR (2.0, 4.0 and 6.0 μg/ml) on the morphological characteristics of four strains of rotifer Brachionus calyciflorus (LZB1, XN2, BNB3 and KMC23) were evaluated. According to the two models of DNA taxonomy, three evolutionary species were discriminated in B. calyciflorus groups. Generally, the morphological features in the four rotifer strains decreased with increase temperature. At 16℃, there were no significant differences in morphological indexes among the four strains. The morphological parameters in KMC23 were minimum at 20℃, and the largest was the strain XN2 at 20 and 24℃. Both of LZB1 and XN2 showed similar responses to temperature change, and reached the smallest at 28℃, which could be attributed to ascribing the two strains into the same evolving entity. The responses of egg parameters to temperature change varied among four rotifer strains. It is thus clear that the identity of cryptic species and/or strain is an important endogenous factor which leads to the variant responses of morphological characteristics in rotifer to temperature. Among four B. calyciflorus strains, the effects of temperature, MC-LR and their interaction were the most significant to the morphological features of LZB1 which could hold the greatest capability of phenotypic flexibility. Under the stress of high temperature, all morphological parameters in LZB1 decreased significantly, however, there were no significant effects of MC-LR concentration to morphological features. At low temperature, the MC-LR at low concentration did not affect those indexes in LZB1, and in contrast, the high concentration of MC-LR decreased most of morphological parameters significantly. In summary, the effects of microcystins in water to the morphological flexibility in rotifer were necessarily constrained by endogenous and exogenous factors.