Microeukaryotic planktons are of great ecological importance, whose composition and diversity will influence the basic functions of ecosystems. However, studies of whether environmental changes affect the community assembly of eukaryotic planktons are relatively scarce, especially in a large scale. Therefore, our goal is to unveil the biogeographic patterns and ecological processes of eukaryotic planktons along the south to north corridor of Fujian coastal sea. In this study, we select five coastal bays along Fujian coastal area and 578 DNA samples were collected. Temperature, salinity, chlorophyll a, nitrate and other nutrients were measured. DNA was extracted and sequenced on the illumine MiSeq platform. 423 Generalists and 603 specialists were identified. We found that (1) generalists occupied wider intraspecific variation and higher niche breadth then specialists, (2) temperature and salinity were most associated with microeukaryotic planktons, (3) the biogeographic patterns were mainly driven by stochastic processes rather than deterministic processes,  (4) the co-occurrence network of specialists was more robust and complex than that of generalists.