The ingestion rates of the heterotrophic protist Polykrikos kofoidii feeding on three different species of Alexandrium were determined by means of incubation experiments in well-plates. In this experiment P. kofoidii was subjected to prey mixtures consisting of A. pseudogonyaulax (strain L4-B9) and A. catenella (strain Alex 5) or A. limii (strain Atay99Shio-02), whereby one prey was dyed with the fluorescent dye CMAC. The dye had no influence on the feeding behaviour of P. kofoidii and thus dye combinations of the same prey mixtures were combined. This dataset contains all data collected within this experiment including cell counts and ingested prey cells of P. kofoidii. The experiments were carried out on January 18, 2023 in the laboratories at the Alfred-Wegener-Institute in Bremerhaven, Germany.