To understand the structural characteristics and functions of cilia in the nephridium of Phascolosoma esculenta, the distribution and morphological structure of cilia were investigated by light and electron microscopy. Cilia are widely present in the nephridium, including the inner face of the nephrostome. Furthermore, the surface of multiciliary cells on the adventitia bears tufts of cilia while the free surface of columnar and cuboidal epithelial cells is sparsely ciliated. Structurally, a cilium can be divided into a ciliary shaft, transitional zone, basal body and ciliary rootlets. Ciliary shaft is composed of a canonical “9+2” microtubule structure and the coated membrane. The peripheral doublet microtubules are continuous with the axoneme of basal body by transitional zone. The area between ciliary shaft and basal body is the transitional zone, where the central microtubules terminate. The cilia are anchored by the ciliary rootlets projecting from the cylindrical basal body, which shows a “9 0” arrangement of microtubules. Cross striations within the conical rootlets have a 70nm periodicity. Rootlets, made up of microfibrils, contain a long rootlet and two short rootlets. It can be probably concluded that cilia in the nephridium are mainly responsible for promoting the flow of the coelomic fluid, improving the function of filtration and directing mature spermatozoa and eggs into the nephridium.