Early molecular trees based on rRNA placed the parasitic or commensal genera (entamoebids) and the flagellate genera (pelobionts) as separate groups that diverged from other eukaryotes very early on, suggesting that the absence of mitochondria was a primitive condition. The absence of dictyosomes in Pelomyxa was also considered primitive, which would separate it from Entamoeba, which has dictyosomes.
The name Archamoebae, from Greek αρχη first, refers to this presumed antiquity. However, studies based on other genes have shown that this placement is an artifact of long-branch attraction. Instead, the Archamoebae are part of the Amoebozoa that have lost their mitochondria, and are particularly close relatives of the slime moulds. It also appears the pelobionts and entamoebids are not separate groups, i.e. Entamoeba and Endolimax developed separately from free-living ancestors.