Viruses are known as important mortality agents of marine microorganisms. Most studies focus on bacterial and algal viruses, and few reports exist on viruses infecting marine heterotrophic protists. Here we show results from incubations initiated with a microbial assemblage from the central Indian Ocean amended with different amounts of organic matter. Heterotrophic flagellates developed up to 30,000 cells/mL in the most enriched incubation, with the peak formed by Cafeteria roenbergensis and Caecitellus paraparvulus. During the peak, C. roenbergensis cells were observed with virus-like particles in the cytoplasm, and 4 days later this taxon could not be detected. Transmission electron microscopy confirmed the viral nature of these particles (280 nm, double-stranded DNA, burst size ~70).