AbstractUnicellular cyanobacterial diazotrophs (UCDs) are important nitrogen (N) fixers in marine ecosystems. However, the top‐down control on UCDs is poorly understood, especially for microzooplankton grazing that is often considered to be the dominant loss factor for primary production in oligotrophic oceans. In this study, we investigated the growth and microzooplankton grazing rates of the major UCD taxa (UCYN‐A1, UCYN‐A2/3/4, UCYN‐B, and UCYN‐C) in the South China Sea and the Luzon Strait using a combination of dilution experiments and quantitative PCR. All UCD taxa were actively grazed by microzooplankton, with higher grazing rates occurring in deeper layers of the photic zone. Microzooplankton grazing rates of UCDs were significantly higher than those of phytoplankton as whole, indicating that UCDs might be preferentially grazed by microzooplankton assemblages. The growth and microzooplankton grazing rates of UCDs were almost balanced, suggesting that a substantial amount of the UCD‐derived N is transferred through the food web via microzooplankton in these regions. Our study highlights the importance of microzooplankton grazing in the fate of UCD‐derived N and indicates that UCDs contribute significantly to the plankton food web in oligotrophic oceans where new N is mainly originated from dinitrogen fixation.