The hypothesis that protists without mitochondria, the so-called Archezoa of Cavalier-Smith, are primitive has received some support from rRNA sequence studies on Microsporidia and Diplomonadida. In spite of the lack of mitochondria the archezoan groups of protists show considerable differences in their organization: mastigont and cytoskeletal system, mitosis, Golgi apparatus, hydrogenosomes. This paper examines the characters of the flagellar apparatus and its associated cytoskeleton to obtain clues used for phylogenetic consideration on the three cited groups of flagellates. Archamoebae of the Pelobiontida order comprising families such as Pelomyxidae and Mastigamoebidae share common features: a rudimentary mastigont system composed of only one basal body giving rise to a poorly motile flagellum and a basal body associated microtubular cone capping the nucleus. No Golgi apparatus has been detected. Metamonada, comprising three orders: Retortamonadida, Diplomonadida, and Oxymonadida, have been tentatively assembled on the basis of the absence of mitochondria, Golgi apparatus, and basal body arrangement. They all have four basal bodies arranged in two pairs with always one recurrent flagellum generally included in a cytostomal depression. The recurrent basal body/flagellum is in relation to recurrent microtubular fibers. However, they display marked differences in their cytoskeletal system and fiber ultrastructure indicating a distant evolutionary relationship. The presence of a corset of microtubules in retortamonads and three microtubular fibers are distinguished in diplomonads, as well as a paracrystalline preaxostyle and axostyle in oxymonads are features that lend support to these groups being highly divergent. Parabasala, comprising the orders Trichomonadida and Hypermastigida, is a monophyletic group with a set of homologous features such as the presence of the same arrangement of four basic basal bodies, the parabasal apparatus (striated fibre supporting Golgi), the microtubular pelta-axostyle complex, the external mitotic apparatus (crypto-pleuro-mitosis), the hydrogenosomes. These three phyla appear distantly related, the Parabasala being a homogeneous group, perhaps also the Pelobiontida, while the Metamonada is heterogeneous and composed of three evolutionary lineages. Additional information such as rRNA and protein sequence data could contribute to a better understanding of the phylogenetic relationships among these groups.
