Despite their importance, little is known about the predators that consume this cyanobacterium and make its biomass available to higher trophic levels. We identify potential predators along a gradient wherein Prochlorococcus abundance increased from near detection limits (coastal California) to >200,000 cell ml-1 (the subtropical North Pacific Gyre). Dinoflagellates and diverse stramenopiles had the highest relative amplicon abundances across the gradient. However, RNA-Stable Isotope Probing experiments involving in situ communities and labelled Prochlorococcus as prey, revealed that the active predators are not appropriately highlighted in conventional amplicon surveys. Our studies exposed choanoflagellates as the active predators of Prochlorococcus, alongside a radiolarian, and within stramenopiles, chrysophytes, dictyochophytes, and specific MAST lineages. In identifying direct consumers of Prochlorococcus we reveal food-web linkages of individual protistan taxa and resolve carbon transfer from the base of marine food webs.