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The Apusozoa comprise several genera of flagellate protozoa. They are usually around 5-20 μm in size, and occur in soils and aquatic habitats, where they feed on bacteria. They are grouped together based on the presence of an organic shell or theca under the dorsal surface of the cell. There are three orders, often treated as separate groups: the apusomonads, ancyromonads, and hemimastigids.

The apusomonads include two genera, Apusomonas and Amastigomonas, and the ancyromonads include one, Ancyromonas. They have two flagella inserted at right angles, near the anterior of the cell. They move by gliding, with one flagellum trailing along the side and one directed to the anterior. The hemimastigids include three genera, Hemimastix, Spironema, and Stereonema. They are also called the spironemids or Hemimastigophora. Each cell has multiple flagella, arranged in rows from the anterior of the cell towards the posterior.

The form of the mitochondria varies between the different orders. Among the apusomonads they have tubular cristae, the ancyromonads flat cristae, and the hemimastigids ambiguous or sacculate cristae. This characteristic was originally considered a good indicator of relationships, but is now known to vary even among close relatives. On molecular trees, the apusomonads and ancyromonads group together, but their relationship to other eukaryotes is uncertain. Cavalier-Smith, in a collaborative paper with Alexandra Stechmann, postulated that Apusozoa belongs in the bikont clade. Although it has sometimes been included in the Rhizaria, based on 18S rRNA gene sequencing, it has been concluded that the Apusozoa are not closely related to other Rhizaria and may be the most divergent bikont lineages.

• David J. Patterson (1999). "The Diversity of Eukaryotes". American Naturalist 145: S96-S124. 
• Cavalier-Smith, T. (2002). "The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa". International Journal of Systematic and Evoluionary Microbiology 52: 297-354. 
• Cavalier-Smith, T.; Stechmann, Alexandra (2003). "The root of the eukaryote tree pinpointed". Current Biology 13 (17): R665-R666. 

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