With the advent of molecular phylogenetics, the morphology-based classification of Porifera has been cardinally changed. However, the relationships between some clusters of Demospongiae, the most diverse sponge class, remain uncertain. An analysis of sponge cell ultrastructures, in particular the flagellar apparatus (kinetid) of choanocytes, may help clarify the evolutionary links in Demospongiae. We studied the kinetid structure of the sponges Spongilla lacustris, Ephydatia fluviatilis and Lubomirskia baikalensis, which belong to the recently established order Spongillida (Heteroscleromorpha). In these sponges, the kinetid of the choanocytes have a uniform structure, consisting of a single kinetosome (without centriole) encircled with a ring of electron-dense bodies producing lateral microtubules. The flagellar transition zone contains a transverse plate with an axosome and a coiled filament. This type of kinetid is similar to that of Haplosclerida representatives, whose morphologic similarities with Spongillida representatives were still not explained. We also discussed the nuclear location in the choanocyte (basal or apical), which correlates to the kinetid structure in Demospongiae. Only three types of flagellar apparatus have been found in Demospongiae up to now, implying that the kinetid is one of the most conservative structures in sponge evolution.