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Abstract Radiolarians are marine protists with a global distribution. Epipelagic radiolarians host photosynthetic endosymbionts, but the identity and specificity of this relationship appears to vary between radiolarian subgroups. While the class Acantharea and the order Collodaria both possess stable and relatively specific relationships with the haptophyte Phaeocystis and the dinoflagellate Brandtodinium nutricula, respectively, the orders Nassellaria and Spumellaria (which comprise the solitary Polycystinea) might have greater flexibility in terms of the identity of their photosymbionts. However, little molecular data has been generated to identify the phytoplankton with which polycystines can associate. Here, we performed short-read 16S and 18S rRNA gene sequencing with universal primers on single polycystine cells collected from the Sargasso Sea to determine common members of the polycystine holobiont. While previous work on polycystine photosymbioses suggested that they almost always exclusively associate with B. nutricula, we determined that polycystines instead associated with a wide diversity of phytoplankton, and the diversity of the polycystine holobiont is distinct from the diversity of environmental samples. Finally, we found that a substantial proportion of the reads associated with cell samples were of opisthokont origin (mostly copepods), revealing other possible interactions between an uncultivable and difficult-to-study protist with its environment.