Planktonic flagellates and ciliates are the major consumers of phytoplankton and bacterioplankton in aquatic environments, playing a pivotal role in carbon cycling and nutrient regeneration. Despite certain unicellular predators using chemosensory responses to locate and select their prey, the biochemical mechanisms behind prey reception and selection have not been elucidated. Here we identify a Ca2+-dependent, mannose-binding lectin on the marine dinoflagellate Oxyrrhis marina, which is used as a feeding receptor for recognizing prey. Blocking the receptor using 20 μM mannose-BSA inhibited ingestion of phytoplankton prey, Isochrysis galbana, by 60%. In prey selection studies, O. marina ingested twice as many 6 μm diameter beads coated with mannose-BSA as those coated with galNac-BSA. When pre-incubated with mannose-BSA, O. marina was no longer able to discriminate between different sugar-coated beads. Thus, these findings reveal molecular mechanisms of protozoan prey recognition. Our results also indicate the functional similarity between cellular recognition used by planktonic protozoa to discriminate between different prey items, and those used by metazoan phagocytic blood cells to recognize invading microorganisms.