Determinants of microeukaryotic biogeography in coastal waters at regional scale remain largely unclear.The coastal northern Zhejian is a complex marine ecosystem with multiple environmental gradients,which isa valuable region for addressing key process conditioning microbial biogeography.We investigated microeukaryotic communities in surface waters from 115 stations in this region using 18S rDNA amplicon sequencing.The microeukaryotic communities were mainly comprised of Dinoflagellata,Ciliophora,Protalveolata,Rhizaria,Stramenopiles and Cryptophyceae.Dinoflagellate and Ciliophora characterized as the most abundant taxa were found dominantly in distinct geographic zones.Detrended correspondence analysis (DCA) revealed that most of the top abundant operational taxonomic units (OTUs) were highly specific for distinct habitat types exhibiting significant environment-conditioned features.While,the cosmopolitan OTUs were rarely relevant with the measured environmental variables.Total phosphorus and suspended particles were major environmental determinants of microeukaryotic α-diversity.Environmental factors,particularly temperature,salinity,pH and silicate were strongly associated with microeukaryotic community composition.Overall,environmental and spatial factors explained 55.92% of community variation in total;in which they shared 34.03% of the community variation,suggesting that spatially-structured environmental variations mainly conditioned the microeukaryotic biogeography in this region.Additionally,dispersal limitation was another important process as evidenced by high pure spatial effects.In summary,our results reveal that spatially structured environmental variation and dispersal limitation are main drivers conditioning microeukaryotic biogeographyin a typical costal area and these traits together with microeukaryotic cell size should be considered when developing a predictive framework for microeukaryotic community dynamics in coastal environments with multiple gradients.