Rhizaria is a heterogeneous assemblage of protists, whose existence is based exclusively on molecular evidence. This supergroup appeared first as the union of the euglyphids and chlorarachniophytes in SSU rRNA gene phylogenies (Bhattacharya et al. 1995). Cavalier-Smith and Chao (1997) showed these taxa to be related to the cercomonad and thaumatomonad flagellates and the plasmodiophorid plant pathogens, and the new phylum Cercozoa was erected to accommodate this assemblage (Cavalier-Smith 1998).

Over the past few years, several other protists of previously unclear affiliation have been shown to be part of this assemblage based on SSU rRNA data. These notably include the testate, filose Gromia oviformis (Burki et al. 2002), the “athalamid”, reticulose Gymnophrys cometa (Nikolaev et al. 2003), the haplosporidian and paramyxid parasites of bivalves (Cavalier-Smith and Chao 2003a), the desmothoracid heliozoans (Nikolaev et al. 2004), and the phaeodarean radiolarians, which are not closely related to Acantharea and Polycystinea (Polet et al. 2004). Various other amoeboid and/or flagellated organisms also belong to Cercozoa, further increasing the morphological heterogeneity of the group (Atkins et al. 2000; Bhattacharya and Oliveira 2000; Kühn et al. 2000; Bulman et al. 2001; Vickerman et al. 2002; Wylezich et al. 2002; Cavalier-Smith and Chao 2003b).

In the meantime, two important lineages of amoeboid protists have been shown to be closely related to the Cercozoa. The first one is the Foraminifera, as demonstrated by actin (Keeling 2001; Archibald and Keeling 2004), polyubiquitin (Archibald et al. 2003), RNA polymerase II (Longet et al. 2003), and revised SSU rRNA (Berney and Pawlowski 2003) analyses. Available data point at Gromiidae (and possibly Haplosporidia) as the closest relatives of Foraminifera (Longet et al. 2004).

The radiolarians are the second important group of protists that has been shown to be related to the Cercozoa-Foraminifera clade. This relationship was first proposed based on SSU rRNA studies (Burki et al. 2002; Cavalier-Smith 2002; Polet et al. 2004), and the term Rhizaria was created by Cavalier-Smith (2002) to name this new supergroup of eukaryotes. The existence of the Rhizaria is now further supported by the first protein data on radiolarians (Nikolaev et al. 2004). The Rhizaria thus includes the majority of filose and reticulose amoebae and most actinopods, plus two parasitic lineages and some flagellates.