Hyperamoeba flagellata is a fresh-water protist of uncertain taxonomic position. It exists in three living forms: as an amoeba, a flagellate and a cyst. The ultrastructure of the flagellated stage of H. flagellata is investigated here by TEM for the first time. Special attention was paid to the structure of the flagellar apparatus. There is one long smooth flagellum only which is directed anteriorly. It emerges from the flagellar basal body (kinetosome) located at the apical end of the cell. Two cones of microtubules extend from the flagellar base towards the nucleus. The outer cone originated from the lateral side of the flagellar kinetosome, while the inner cone arises from an MTOC associated with the flagellar kinetosome by a short fibrillar rootlet. The second (barren) kinetosome lies ventrally and is directed to the right side of the cell. It has two microtubular rootlets which pass laterally in the same direction. The microtubular cones overlap the anterior end of the nucleus. A dictyosome lies between the basal bodies and the nucleus. Mitochondria with tubular cristae have an electron dense core which is orientated in a longitudinal axis. The structure of the flagellate stage of H. flagellata is compared with flagellated cells of protostelids and cercomonads. It is proposed that this organism may represent a link between protostelids and cercomonads.