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Protists, as integral constituents of the plant microbiome, are posited to confer substantial benefits to plant health and performance. Despite their significance, protists have received considerably less attention compared to other constituents of the plant microbiome, such as bacteria and fungi. To investigate the diversity and community structure of protists in sorghum leaves and roots, we employed amplicon sequencing of the eukaryotic 18S rRNA gene in 563 leaf and root samples collected from 57 locations across China. We found significant differences in the diversity and community structure of protists in sorghum leaves and roots. The leaf was taxonomically dominated by Evosea, Cercozoa and Ciliophora, while the root was dominated by Endomyxa, Cercozoa and Oomycota. The functional taxa of protists exhibited notable differences between leaves and roots, with the former being predominantly occupied by consumers and the latter by parasites. The community composition of protists in the leaf was predominantly influenced by mean annual precipitation, whereas soil pH played a more significant role in the root. The present study identified the most abundant and distributed protists in sorghum leaves and roots and elucidated the underlying factors that govern their community structure. The present study offers a novel perspective on the factors that shape plant‐associated protist communities and their potential roles in enhancing the functionality of plant ecosystems. [ABSTRACT FROM AUTHOR]