The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean, and sampled the surface of oceanic waters at 249 locations, resulting in the collection of nearly 58,000 samples. The expedition was designed to systematically study corals, fish, plankton, and seawater, and included the collection of samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide flow cytometry data obtained for pico- and nano-phytoplankton, bacteria and viruses. Samples were fixed with Glutaraldehyde, kept onboard in liquid nitrogen and then stored at -80°C back in the laboratory. They were then analyzed unstained for phytoplankton using a FACS Canto II flow cytometer and stained using SYBR Green-I for bacteria and viruses.