Abstract:[Background] Zabuye Lake (ZL) is a saline-alkali lake in Xizang, with high concentrations of CO32−, HCO3−, and Na+. There are few studies involving eukaryotic plankton diversity in this lake. [Objective] To clarify the diversity and composition of eukaryotic plankton and the trophic mode of fungi in ZL. [Methods] High-throughput sequencing of the V5–V7 region of the 18S rRNA gene was employed to analyze the community structure and species diversity of eukaryotic plankton in ZL. Spearman correlation coefficients were calculated to measure the correlations of genera with the chemical characteristics of lake water. FUNGuild was used to predict the trophic mode of fungi. [Results] Illumina sequencing yielded 25 genera of eukaryotic plankton belonging to 20 classes, 12 phyla, and 2 kingdoms. The dominant phyla were Aphelidea (0.12%−51.84%), Nucleariidae-Fonticula (0%−91.70%), Ascomycota (1.38%−9.04%), and Basidiomycota (0.20%−10.16%). The common genera included Nuclearia (0%−91.70%), Fusarium (1.38%−4.32%), Paraphelidium (0%−4.57%) and Homalogastra (0%−4.39%). Homalogastra, Protosporangium and Nuclearia showed significantly positive correlations with Na+, K+, and Ca2+ concentrations and total salinity, and they had significantly negative correlations with temperature, total phosphorus, total organic carbon, and pH. The functions of planktonic fungi in each sample site were mostly unknown and saprotrophic fungi (1.38%−5.24%) were present in all the sample sites. [Conclusion] The community structure of eukaryotic plankton in ZL was similar to that in other saline-alkali lakes. The dominant phyla were Ascomycetes and Basidiomycota, with the presence of Aphelidea and Nucleariidae-Fonticula. The community structure was closely related to the salt concentrations of ZL. Most of the planktonic fungi in this lake were saprotrophs.