The typical cercomonad structure (based on original investigations of Heteromita sp., Cercomonas agilis and literature data) is as follows: the amoeboflagellate cell is covered by only a distinct glycocalyx; there are two flagella, extrusomes, microbodies, mitochondria with vesicular cristae, and the nucleus has a sharp end directed towards the basal bodies. Absolute orientation of the flagellar apparatus reveals an anterior basal body directed in a forward or ventral direction, and the posterior basal body is located on the ventral side and is directed to the right. There are 2–4 lateral microtubular rootlets, a layered structure and a nuclear fibrillar rootlet. A dictyosome occupies the dorsal position. The life-cycle of cercomonads includes a plasmodial stage. Comparison of cercomonad morphology and life-cycles with those of myxomycetes (predominantly with zoospores of protostelids) and Hyperamoeba flagellata (a fresh-water protist of uncertain taxonomic position) reveals the homology of structures in the flagellar rootlet system; the same absolute orientation of the flagellar apparatus and dictyosome; and mitochondria with vesicular cristae. Homology of the main stages in the life-cycles of all three groups has been also proposed. The relationship of cercomonads and protostelids has been confirmed by new ultrastructural data, and H. flagellata is considered as a bridge between these two groups. This view contradicts molecular data which usually demonstrates a long distance between cercomonads and myxomycetes.