Red tides are a major public hazard in the global oceans. The coast of the East China Sea is the sea area where red tide disasters are the most frequent and serious in China. In order to accurately grasp the occurrence of red tides in the coastal waters of the East China Sea, and to understand the microbial communities in the waters during the occurrence of red tides in the East China Sea, a special survey of red tides in the coastal waters of Zhejiang, China was carried out in June 2018. The results showed that nutrient concentrations of N and P were generally high in this area, DIN concentrations in most areas exceeded the permitted limit of Chinese seawater quality grade I. There were significant differences in dissolved oxygen, pH, COD, chlorophyll and phytoplankton abundance of red tides. During the investigation, red tides were found in the waters near the Yushan Islands. The content of chlorophyll a was 42.12mg/m3, the cell abundance of phytoplankton was 8.16×108/L, and the abundance of Prorocentrum edulis accounted for 98.5%. The Illumina MiSeq sequencing platform was used for 16s high-throughput sequencing of water microorganisms, and a total of 16 bacteria were identified. Proteobacteria is the first dominant phylum, followed by Cyanobacteria and Bacteroides. Some differences in bacterial community compositions between HAB and the nearby seawater were observed. The predominant bacteria in the red tide occurrence area were Proteobacteria, comprising 46.1% of the relative abundance; while the predominant bacteria in the nearby sea area, comprising 42.0% of the relative abundance.