Seven species of polycystine radiolarians and one phaeodarian species were investigated in order to determine the diversity of their associate organisms and their species specificity. Twelve partial 18S ribosomal DNA (rDNA) sequences were obtained showing a high diversity of associates, both within spumellarian and nassellarian radiolarians and among species. Two of the sequences obtained are highly similar to Scrippsiella, a dinoflagellate genus already reported as a symbiont of polycystine radiolarians. Nine of the new 18S rDNA sequences group with various alveolates. Some of these groups include parasites, such as the lethal endoparasite Amoebophrya, while others consist of non-annotated novel organisms found worldwide in various types of marine environments. We also obtained a sequence from a bacillariophytan highly similar to the 18S rDNA of the diatom species Diatoma tenue, which may derive from radiolarian food. Additionally, this is the first study to report on a phaeodarian associate.