Earlier protist classifications placed all amoebae possessing lobose pseudopodia in the class Lobosea, belonging to the superclass or phylum Rhizopoda (Levine et al. 1980; Bovee 1985). However, based on ultrastructure and life cycle studies, the amoebae and amoeboflagellates with discoidal mitochondrial cristae and without typical dictyosomes were excluded from the Lobosea and placed in the class Heterolobosea (Page & Blanton 1985; Page 1987). The distinction of both classes was confirmed later by analysis of small-subunit ribosomal RNA (SSU rRNA) sequences (Clark & Cross 1988; Hinkle & Sogin 1993). Futhermore, the position of pelobionts- the free-living amitochondriate amoebae- is debated. For example, this group was considered either as a separate phylum (Margulis 1974; Margulis et al. 1990), as a separate class within the Rhizopoda (Page 197), as an order within the Lobosea (Bovee 1985), or placed in the phylum Archamoebae, among early diverging amitochondriate eukaryotes (Cavalier-Smith 1987, 1993; Corliss 1994). Another group of amitochondriate amoebae, the entamoebids, viewed by some as the model of primitive eukaryotes (Bakker-Grunwald & Wostmann 1993) was transferred from Lobosea to the Archamoebae (Cavalier-Smith 1987) or later placed in a separate plylum, the Entamoebia (Cavalier-Smith 1993). Early SSU rRNA-based phylogenies suggested independent origins for pelobionts, entamoebids, and other lobose amoebae (Sogin 1991; Hinkle et al. 1994; Sims, Rogerson & Aitken 1999), supporting their separation into different classes or phyla. Based on ultrastructural data and following ribosomal RNA phylogenies, recent protist classifications widely accept the polyphyly of lobose amoebae, splitting them into at least three taxonomic groups (Hausmann & Hulsmann 1996; Lee, Leedale & Bradbury 2000).
A recent opposite view proposes that all lobose amoebae, within the exception of Heterolobosea, are monophyletic (Cavalier-Smith 1998). This view is based molecular evidence that the pelobionts and entamoebids have lost their mitochondria secondarily (Clark & Roger 1995) and that they group together with lobose amoebae in some revised ribosomal RNA phylogenies (discussed in Cavalier-Smith & Chao 1996, and Cavalier-Smith 2000, and demonstrated later by Bolivar et al. 2001, and Milyutina et al. 2001). The phylum Amoebozoa Luhe, 1913 was emended to group together the naked and testate lobose amoebae, the pelobionts, the entamoebids, and the Mycetozoa (Cavalier-Smith 1998). The latter group was included into Amoebozoa based on analysis of actin and actin-related proteins (Kelleher, Atkinson & Pollard 1995; Bhattacharya & Weber 1997; Schafer & Schroer 1999). This was recently confirmed by the combined analysis of nuclear (Baldauf et al. 2000) and mitochondrial (Forget et al. 2002) protein sequences of the lobosean Acanthamoeba and the slime molds Dictyostelium and Physarum. A common origin for Entamoeba, Mastigamoeba, and Dictyostelium was also inferred from combined analysis of EF-1a and EF-2 sequences (Arisue et al. 2002) and is strongly supported by the analysis of 123 genes obtained from EST libraries (Bapteste et al. 2002). However, none of these studies includes representatives of typical free-living, lobose amoebae (order Euamoebida).