[Objectives] Recently, many ciliopathy-associated proteins are found in the basal body of cilia, and these proteins are also located in ciliates, Euplotes amieti. Ciliates have thousands of basal bodies of cilia and a complicated microtubular cytoskeleton, therefore, it is an ideal material for studying the interaction between the basal body and the microtubular cytoskeleton. [Methods] In this experiment, immunofluorescence and immuno-electron microscopy were used to observe the cellular and subcellular localization of Centrosomal protein 43 (CEP43) and Coiled-coil domain-containing 13 protein (CCDC13) in Euplotes amieti. [Results] The results showed that the cilia microtubular organelles of Euplotes amieti were composed of the adoral zone of membranelles, caudal cirrus, marginal cirrus, frontoventral cirrus, transverse cirrus, radiating microtubule, and dorsum bristle (Fig. 2). Immunofluorescence showed that CCDC13 was mainly located in the basal body and rod of cilia microtubular organelles and the silverline system (Fig. 3a, b), while CEP43 was mainly located in the basal body of cilia microtubular organelles, and cirrus accessory microtubules and nucleus (Fig. 3c). CEP43 and γ-tubulin were co-localized in the regions mentioned above (Fig. 4), while CCDC13 and γ-tubulin were only located in the same regions on the ventral side of Euplotes amieti (Fig. 5a, b). On the dorsum, CCDC13 was located in the silverline system (Fig. 5d), while γ-tubulin was located in the basal body of the dorsal cirri (Fig. 5e). During the cell division, CEP43 was not located in the nucleus, but in the basal body and the adoral zone of membranelles (Fig. 6a, b), while CCDC13 was observed in the adoral zone of membranelles (Fig. 6c, d). Further, the immuno-electron microscopy showed that CEP43 and CCDC13 were located in the basal bodies of the cilia, the adoral zone of membranelles, the base of the frontoventral cirrus, and the base of the transverse cirrus (Fig. 7), and the amount of colloidal gold at the base of frontoventral cirrus of CCDC13 was much more than that of CEP43 (Fig. 7h), while CCDC13 was not observed in the nucleus (Fig. 7j). [Conclusion] 1) CCDC13 and CEP43 are involved in the formation of cilia and basal body; 2) CEP43 can form complexes with CAP350 to provide attachment points for microtubule extension; 3) the excess CEP43 will be regulated and recruited to the nucleus after the formation of cilia; 4) the CCDC13 participates in the formation of the silverline system, in addition, it will affect the rate of microtubule regeneration. However, in order to increase the regeneration off the anterior longitudinal microtubules of Euplotes amieti during the growth period, CCDC13 is not required. The results provide basic data for further research on the roles and mechanisms of the above proteins in regulating and maintaining the assembly and stability of the cortical microtubule cytoskeleton in hypotrichous ciliate.