The processes of encystment and excystment of the hypotrichous ciliate (Euplotes encysticus), were investigated using interference contrast microscopy and real-time quantitative PCR (Q-PCR). Results showed that the microtubular organelles were always in non-assembly and~assembly functional states; furthermore, the activity of the contractile vacuole during excystment played an important role in reassembly of cortical microtubular organelles and cellular activities, and meanwhile, the expression level of -、-和-tubulin genes changed relatively. During the dedifferentiation of the cortical microtubular organelles, cells formed the non-kinetosome-resorbing cysts and the expression of -、-和-tubulin genes showed a downward trend. During the re-differentiation of the cortical microtubular organelles, oral and somatic ciliature formed in order and cells rotated inside the cyst and soon after excysted to vegetative cells, while the gene expression of -、-和-tubulin showed an increasing tendency. During the whole process, the gene expression quantity from more to less were-、-和-tubulin, and the initial copies of the former two were much more than the latter's. It was revealed that during the processes of encystment and excystment of (Euplotes encysticus) with the differentiation of the cortical microtubule organelles, -、-和-tubulin gene were always in the different functional states relatively intracellular, as well as the -tubulin gene which works as microtubule organizing center.