The kinetid (flagellar/ciliary apparatus) of eukaryotic cells is an important source of phylogenetic information. It was found to be a prospective morphological phylogenetic marker in sponges, since its arrangement in choanocytes is congruent with the topology of the phylogenetic trees. However, investigation of the kinetid of sponge larval cells remains fragmentary. Here, we report the results of an ultrastructural study on the larval kinetids of the freshwater sponges Eunapius fragilis and Lubomirskia baikalensis (Demospongiae: Spongillida). Their kinetids were found to comprise a kinetosome associated with an accessory centriole and linked to the nucleus by a simple fibrillar root. The kinetosome bears a transverse cytoskeleton: filamentous train and microtubules which radiate from a microtubule organising centre (MTOC) shaped as a large hollow foot. In the short transition zone, between the central axonemal microtubules and kinetosome, a transverse plate with an axosome (central thickening) occurs. We have reviewed the kinetids of different sponge larvae to reconstruct the ancestral state of these traits. Thus, we suggest that spongillids retain the plesiomorphic characteristics of roots and an accessory centriole. But they possess the peculiarities of the transition zone, transverse cytoskeleton and MTOC structure.