Polycystines (spumellarians, nassellarians, and collodarians), phaeodarians, and acantharians are marine planktonic protists that have been conventionally and collectively called "radiolaria". Recent molecular phylogenetic studies revealed radiolarian polyphyly with phaeodarians being a separate offshoot. Collodarians and nassellarians are also shown to form a monophyletic group, but other aspects of radiolarian phylogeny, such as interrelations among polycystines and acantharians, remained uncertain. Here, we present molecular phylogenetic analyses including new ribosomal RNA sequences from ten spumellarians and nine nassellarians, based on Bayesian and maximum-likelihood methods. Results indicate that the Polycystinea is a paraphyletic group, with Bayesian analysis suggesting that spumellarians form a clade with acantharians. The heliozoan-like protist Sticholonche appears as a sister to the spumellarian clade. The nassellarian Eucyrtidium is located outside the clade including the other nassellarians and collodarians. The mineralogy of the test of extant radiolarians and the tree topology obtained in this work suggest that acantharians and spumellarians evolved from an ancestor with a siliceous skeleton. Collodarians and nassellarians form a well-supported clade and one might infer from the fossil record that they may have diverged between the Jurassic and the Eocene.