Brown tides have occurred in the Bohai Sea of China since 2009 and caused serious losses in aquaculture. In recent years, phytoplankton identification has been greatly promoted by the development of high-throughput sequencing technologies. In this study, V4 region of 18S rDNA was used as the target gene to design the primer V4 (F/R), and high-throughput sequencing technology was adopted to evaluate the diversity of composition and characteristics of the eukaryotic phytoplankton community