The amitochondrial flagellates comprise the Archamoebae, the Metamonad
a (orders: Retortamonadida, Diplomonadida, Oxymonadida) and the Paraba
sala. Molecular rDNA sequence comparison has shown that the diplomonad
s are very ancient and placed at the base of the tree, but the positio
n of the parabasalids before or after the Euglenozoa and other mitocho
ndriate protists is not definitively determined and such molecular dat
a are required to place the other groups. Common cytological features
such as one basal body and a basal body-nucleus connector show that th
e mastigamoebids or Archamoebae are an evolutionary lineage. The metam
onad grouping is heterogenous; the three orders have in common two pai
rs of basal bodies, no Golgi and could be poly- or paraphyletic. The P
arabasala is an evolutionary lineage with a large set of homologous cy
tological characters. A biochemical study of the cytoskeletal structur
es such as costa, parabasal fibre, preaxostylar fibre and undulating m
embrane in trichomonads reveals a large diversity in the protein compo
sition among the genera that fits with the large distance between the
taxa estimated by rDNA sequencing. Molecular comparison in seven trich
omonad genera indicates that the Trichomonadinae and Tritrichomonadina
e form two divergent branches, the genera Hypotrichomonas and Monocerc
omonas are now incorporated in the tritrichomonad branch, and Trichomi
tus is at the bifurcation of the two branches. This scheme is differen
t from the classic tree but not incompatible with it.