Any discussion of the origin of Metazoa during the last 150 years and particularly in the recent years when the sister relationship of choanoflagellates and Metazoa was unambiguously shown by molecular phylogeny refers to the similarity of sponge choanocytes to choanoflagellates. These two types of collared radially symmetric cells are superficially similar with respect to the presence of microvilli around a single flagellum and flat mitochondrial cristae which are common for many eukaryotes. But a comparison of the most informative structure having a stable phylogenetic signal, the flagellar apparatus or kinetid, has been neglected. The kinetid is well studied in choanoflagellates and is rather uniform, but in choanocytes this structure has been investigated in the last five years and is represented by several types of kinetids. Here we review the kinetid structure in choanocytes of Porifera to establish the most conservative type of kinetid in this phylum. The detailed comparison of this kinetid with the flagellar apparatus of choanoflagellates demonstrates their fundamental difference in many respects. The choanocyte kinetid contains more features which can be considered plesiomorphic for the opisthokonts than the kinetid of the choanoflagellates. Therefore, the hypothesis about the origin of Porifera, and consequently of all Metazoa directly from choanoflagellate-like unicellular organism is not confirmed by their kinetid structure.