CEP43 is a centriole satellite protein involved in ciliogenesis. Although centriole satellites are involved in centrosome and cilium-related protein trafficking, their functions related to ciliary assembly and maintenance of ciliary microtubule stability remain unclear. In this study, the function of the CEP43 gene in Euplotes amieti was investigated by interfering with its expression using RNAi. As a result, expression levels of the ciliary assembly-related proteins BBS8 and IFT88 were down-regulated. Swimming speeds also decreased and the Euplotes were only able to spin in circles, which suggested that the CEP43 protein is an important protein involved in ciliary motion. Further observations of Euplotes amieti microstructure and ultrastructure via immunofluorescence and transmission electron microscopy revealed that CEP43 not only participated in the formation of the ventral ciliary basal body, but also played an important role in the maintenance of cortical microtubules, which is fundamental for the morphological structure of Euplotes amieti.