ABSTRACT Amitochondriate organisms are present in several eukaryotic lineages and usually inhabit anoxic and hypoxic environments. They are free-living, symbiotic or parasitic. Several lineages of flagellates comprise exclusively amitochondriate species: metamonads (retortamonads, two genera; diplomonads, ten genera; and oxymonads, eleven genera), pelobionts (five genera), and parabasalids (trichomonads, forty-six genera; and hypermastigids, thirty-four genera). Some other groups contain the occasional amitochondriate species. The ultrastructure of many species has been well explored. Such studies have defined the characteristic features of each group, but many genera remain to be studied. No organelles of energy metabolism have been recognized in metamonads and in pelobionts, while parabasalids have hydrogenosomes. Metabolic biochemistry has been studied only in a few, primarily parasitic, species of amitochondriate flagellates. Amitochondriate energy metabolism is either not compartmentalized, as in diplomonads (type 1), or shows a hydrogenosome/ cytosol compartmentation, as in trichomonads (type II). It remains to be established whether other amitochondriate flagellate groups also belong to these types. Molecular studies indicate that the absence of mitochondria in diplomonads and trichomonads is secondary. Phylogenetic reconstructions based on ribosomal RNA (rRNA) and certain protein sequences are in agreement with a monophyly of diplomonads and parabasalids. The status of the other amitochondriate flagellate groups has not been resolved yet. The evolutionary emergence of amitochondriate groups in eukaryotic phylogeny remains an open question.