The excavates are a major assemblage of protists, often known as Excavata. The phylogenetic category Excavata contains a variety of free-living and symbiotic forms, and includes some important parasites of humans. Many excavates lack 'classical' mitochondria - these organisms are often referred to as 'amitochondriate', although, most, perhaps all, retain a mitochondrial organelle in greatly modified form. Others have mitochondria with tubular, discoidal, or in some cases, laminar cristae. Most excavates have two, four, or more flagella and many have a conspicuous ventral feeding groove with a characteristic ultrastructure, supported by microtubules.
  Giardia lamblia, a parasitic diplomonad
  Giardia lamblia, a parasitic diplomonad

However, various groups that lack these traits may be considered excavates based on genetic evidence (primarily phylogenetic trees of molecular sequences).

Excavates are classified into four major subgroups at the phylum/superphylum level. These are shown in the table below.

Superphylum Phylum Representative genera Description
Discoba Euglenozoa e.g. Euglena, Trypanosoma Many important parasites, one large group with plastids (chloroplasts)
Percolozoa (Heterolobosea) e.g. Naegleria, Acrasis Most alternate between flagellate and amoeboid forms
Loukozoa (Jakobida) e.g. Jakoba, Reclinomonas Free-living, sometimes loricate flagellates. Some amitochondriate members
Metamonada Preaxostyla e.g. Oxymonads, Trimastix Amitochontriate flagellates, either free-living (Trimastix) or living in the hindguts of insects
Fornicata e.g. Giardia, Carpediemonas Amitochondriate, mostly symbiotes and parasites of animals.
Parabasalia e.g. Trichomonas Amitochondriate flagellates, generally intestinal commensalism of insects. Some human pathogens.

Heterolobosea (Percolozoa) and Euglenozoa appear to be particularly close relatives, and are united by the presence of discoid cristae within the mitochondria (Superphylum Discicristata). More recently a close relationship has been shown between Discicristata and Jakobida. Most jakobids have tubular cristae, like most other protists, while the metamonads are unusual in having lost classical mitochondria - instead they have 'hydrogenosomes', 'mitosomes' or uncharacterised organelles. In addition to the groups mentioned in the table above, the genus Malawimonas is generally considered to be a member of Excavata owing to its typical excavate morphology, and phylogenetic affinity to excavate groups in some molecular phylogenies. However, its position among excavates remains elusive.

Excavate relationships are still uncertain; it is possible that they are not a monophyletic group. The monophyly of the excavates is far from clear, although it seems like there are several clades within the excavates which are monophyletic.

Certain excavates are often considered among the most primitive eukaryotes, based partly on their placement in many evolutionary trees. This could encourage proposals that excavates are a paraphyletic grade that includes the ancestors of other living eukaryotes. However, the placement of certain excavates as 'early branches' may be an analysis artifact caused by long branch attraction, as has been seen with some other groups, for example, microsporidia.

Alastair G. B. Simpson (2003). "Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata". International Journal of Systematic and Evolutionary Microbiology 53: 1759–1777.
Cavalier-Smith, T. (2002). "The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa". International Journal of Systematic and Evolutionary Microbiology 52: 297–354.
Laura Wegener Parfrey, Erika Barbero, Elyse Lasser, Micah Dunthorn, Debashish Bhattacharya, David J Patterson, and Laura A Katz (December 2006). "Evaluating Support for the Current Classification of Eukaryotic Diversity". PLoS Genet. 2 (12): e220.
Naiara Rodríguez-Ezpeleta, Henner Brinkmann, Gertraud Burger, Andrew J. Roger, Michael W. Gray, Hervé Philippe, and B. Franz Lang (August 2007). "Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans". Curr. Biol. 17 (16): 1420-1425.