DNA metabarcoding on single organism is a promising approach to clarify the biological interactions (e.g., predator-prey relationships and symbiosis, including parasitism) of difficult-to-culture protists. To evaluate the effectiveness of this method, Radiolaria and Phaeodaria, which are ecologically important protistan groups, were chosen as target taxa. DNA metabarcoding on single organism focused on the V9 region of the 18S rRNA gene revealed potential symbionts, parasites, and food sources of Radiolaria and Phaeodaria.