Marine microbial flagellates are a highly heterogeneous group of protists with high biodiversity and multiple trophic modes. They occupy broad niches in global marine ecosystem and play essential roles in the biogeochemical cycles. However, little is known about the distribution of the diversity and community structure of the microbial flagellates in a regional marine area, especially the relationship between their biogeographic distribution and the environmental factors. The East China Sea (ECS) is a marginal sea with sloping topography, leading to a wide coastal area and its adjacent open continental shelf area. The hydrological conditions display gradient changing patterns from the coastal area to the shelf area in the ECS, which could affect the microbial flagellates' communities differently, but is so far understudied. Thus, the ECS region provides a suitable system for the study of the relationship between environmental conditions and microbial flagellates' communities. In order to adequately describe the diversity and community structure of the microbial flagellates, as well as the environmental factors that shape and drive their biogeographic distribution patterns, a comprehensive investigation on the microbial flagellates' communities using combined methods of high-throughput sequencing of eukaryotic 18S rRNA gene V4 region and traditional microscopic observation was conducted in the ECS in spring and autumn, 2019. Intensive exploration also attempted using multiple statistical analyses on interpretation of the relationships between environmental factors and structure of microbial flagellates' communities. The main findings are as follows:Firstly, the average abundance of the nano-sized flagellates in the ECS was 2.27×10³ cells/mL, which decreased with increasing distance from the shore. The heterotrophic nano-sized flagellates were dominant at the bottom layer of seawater while the surface seawater was dominated by the pigmented ones. Secondly, the community alpha diversity reflected the community stability and adaptability to environmental conditions, with higher Shannon diversity index both at the bottom seawater and in the shelf area than those at the surface seawater and in the coastal area, respectively. This indicated that the relatively stable environmental characteristics and environmental heterogeneity among different patches in the bottom layer and shelf area might cause sufficient competition and niche differentiation of the community, and thus led to higher biodiversity. Thirdly, different taxa groups of microbial flagellates owned unique nutritional modes and relatively fixed size fractions. The relative richness[numbers of the Operational taxonomic units (OTUs)] and relative abundance (numbers of the sequencing reads) of various taxa were different. Alveolata were the most abundant and diverse taxa in the studied area. Archaeplastida, Hacrobia, and Stramenopiles displayed high relative abundance and richness in the pico-sized flagellates' community, while Rhizaria showed high relative richness mostly in the nano-sized community. Lastly, the potential correlation between the microbial flagellates' communities and environmental factors depended on the degree to which the biological community matched with or adapted to the changing environmental conditions. Different taxa showed different responses to the environmental factors such as temperature, salinity, and dissolved oxygen, etc. This led to the obviously seasonal dynamics and biogeographic distribution patterns of the community composition. Moreover, the geographic distances had an impact on the dispersal limitation of the microbial flagellates' community, which might also result in spatial difference of the community. Specifically, the similarity of the community composition was greatly reduced with the increasing of the environmental heterogeneity and geographical distance. Overall, the findings of this study contribute to improve our understanding of the diversity, community structure, and affecting factors of marine microbial flagellates in the ECS, and to promote the research of marine flagellates from the phenomenon to the process and the mechanism.