The molecular phylogenetic tree of Eukaryotes was the subject of important changes during the last few years. In its most recent form, the tree comprises six to eight supergroups and a number of smaller, independent lineages (Baldauf 2003). It has been proposed that its root should be placed between the Eukaryotes ancestrally possessing a single flagellum (Opisthokonts + Amoebozoa), and those ancestrally possessing two flagella - the Bikonts (Stechmann and Cavalier-Smith 2003). Within this framework, the majority of amoeboid protists branches within one of the two supergroups Amoebozoa and Rhizaria (Nikolaev et al. 2004). Molecular phylogenies of these two supergroups, based on small-subunit ribosomal RNA and actin gene sequences, are presented here.