AbstractThe ultrastructure of the ciliary apparatus of multiciliated epidermal cells in larval and adult sipunculids is described and the phylogenetic implications discussed. The pelagosphera of Apionsoma misakianum has a dense cover of epidermal cilia on the head region. The cilia have a long, narrow distal part and two long ciliary rootlets, one rostrally and one vertically orientated. The adult Phascolion strombus has cilia on the nuchal organ and on the oral side of the tentacles. These cilia have a narrow distal part as in the A. misakianum larva, but the ciliary rootlets have a different structure. The first rootlet on the anterior face of the basal body is very short and small. The second, vertically orientated rootlet is long and relatively thick. The two ciliary rootlets present in the larval A. misakianum are similar to the basal metazoan type of ciliary apparatus of epidermal multiciliated cells and thus likely represent the plesiomorphic state. The minute first rootlet in the adult P. strombus is viewed as a consequence of a secondary reduction. No possible synapomorphic character with the phylogenetically troublesome Xenoturbella was found.