The ingestion rates of the heterotrophic protist Polykrikos kofoidii feeding on two different species of Alexandrium were determined by means of incubation experiments in well-plates. In this experiment P. kofoidii was subjected to monoalgal prey consisting of either A. pseudogonyaulax (strain L4-B9) or Alexandrium catenella (strain Alex 5). This dataset contains all data collected within the experiment including cell counts and ingested prey cells of P. kofoidii. The experiments were carried out between December 2 and 5, 2022 in the laboratories at the Alfred-Wegener-Institute in Bremerhaven, Germany.