Abstract: Marine microbial flagellates are a very important group of microbial eukaryotes that play essential roles in the structure and function of marine ecosystems. Microbial communities are usually composed of a few dominant species and many rare species, of which the distribution pattern is also very common in marine microbial flagellate communities. Their inherent characteristics may have different effects on the community biogeographic distribution pattern and ecosystem functions. However, the two different sub-communities were not distinguished in most studies, and the understanding of their distribution patterns, response to environmental and spatial factors, and ecological status in the overall community was very limited. This study conducted high-throughput sequencing of eukaryotic 18S rRNA gene V4 region to comprehensively investigate the distribution characteristics of dominant and rare species in the microbial flagellate communities in 3 subtropic-tropic marine areas in China. The relationships between both environmental and spatial factors and two subcommunities were also explored. The neutral model was used to reveal the importance of neutral process in community assembly. Finally, the ecological status of two sub-communities in the overall community was compared using co-occurrence network analysis. The results showed different characteristics in diversity and species composition of the dominant and rare sub-communities in the 3 sea areas, which led to comparable biogeographic distribution patterns. This was related to the different degrees of the driving effects of environmental and spatial factors on different sub-communities. The neutral model reflected the important role of the neutral process in the two su-bcommunities. Finally, the cooccurrence network revealed the overlapping but different niches of the two sub-communities, which formed coexistence of species and thus maintained the community stability. Among these, the rare taxa, with a higher degree of connectivity and a higher proportion of the number of keystones species, played important roles in the network. Overall, the findings of this study revealed the distribution patterns and community assembly mechanisms of dominant and rare species of microbial flagellates in the coastal waters of China, and provided a theoretical basis for further understanding of the community structure, biogeographic distributions, and ecological processes of marine microbial flagellate communities.