Rhizaria is a supergroup of eukaryotes established solely on molecular characters. It comprises several groups of uncultivable free-living organisms such as foraminiferans, radiolarians, gromiids, cercozoans as well as the haplosporidians (animal parasites) and plasmodiophorids (plant parasites). The phylogenetic relationships of the major rhizarian lineages remained unresolved for the recently established Rhizaria. One of the major difficulties for resolving its phylogeny is the overall lack of data. Most of the data available for the group are 18S rDNA sequences and a handful of genes such as tubulin and actin for selected species. To clarify the deep phylogenetic relationships of the group using a phylogenomic approach, dozens of transcriptomes were sequenced from species in all major lineages. The analyses presented here revealed a close relationship between Foraminifera and polycystine radiolarians. Rhizarian animal and plant parasites evolved independently and do not represent a monophyletic clade. Four major clades were recovered: Retaria, Ascetosporea and Apofilosa, Phytorhiza and Filosa.