Within the holoplanktonic protists group Radiolaria, the Class Phaeodarea is today represented by several hundreds species. The phaeodarian skeletons consist of opaline silica as well as organic matter and are very fragile and vulnerable to dissolution. Their tests are therefore rarely found in the fossil records; this has caused uncertainty with regard to their phylogenetic evolution. In this study, small, solitary phaeodarian species, namely, Protocystis xiphodon (Haeckel), Challengeron diodon Haeckel and Conchellium capsula Borgert were examined using molecular techniques in order to clarify the phylogenetic position of the Phaeodarea. The phylogenetic trees obtained from the neighbor-joining, maximum-parsimony and maximum-likelihood methods of analysis showed that all phaeodarians formed a monophyletic group within the Phylum Cercozoa. This result contradicts Haeckel's classical taxonomy, wherein the phaeodarians were grouped along with the polycystines, i.e., nassellarians and spumellarians, and the acantharians under the common name "Radiolaria". Within the cercozoan clade, the Phaeodarea were closely related to the euglyphid and pseudodifflugid testate amoebae and the desmothoracid heliozoans. The tests and skeletons of both the phaeodarians and the euglyphid testate amoebae resemble each other in their chemical composition and construction. The similarities in the morphologic features may suggest that they are sisters as the Phylum Cercozoa in which leading from molecular methods. (c) 2006 Elsevier B.V All rights reserved.