The protomonadina comprise a heterogenous group of flagellates with one or two, rarely with up to four flagellae. Two groups are of special interest. Choanoflagellates (see below) possess one single, long flagellum which is along the half length ensheathed by a collar. In the ultrastructure this is consisting of fathom-like filaments. It therefore reminds of the poriferan choanocytes and the basic excretory organ of bilaterians, the protonephridium. This suggests choanoflagellates to be the common ancestor of multicellular animals.
Kinetoplastids exhibit a large, specialized mitochondrion, the kinetoplast, which lies at the basis of the flagellum. This mitochondrion contains the highest amount of DNA amongst so far known mitochondria and is therefore thought to represent the closest relative to the bacterial ancestors of mitochondria which may be found in the alpha subdivision of Proteobacteria (with Paracoccus denitrificansas closest relative)