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Citrus exocortis viroid (CEVd) and citrus bark cracking viroid (CBCVd) are two important viroids that infect citrus plants and frequently occur as mixed infections in orchards. However, the mechanism of antagonism between the two viroids in mixed infections remains unclear. The CEVd/CBCVd–citron system and small RNA sequencing (sRNA‐seq) were used to study the antagonism. When CBCVd was inoculated before CEVd, the CEVd titre was significantly reduced and the symptoms were attenuated. Viroid‐derived sRNAs (vd‐sRNAs) from CEVd and CBCVd were predominantly 21‐nucleotide (nt) and 22‐nt in length and had similar 5′ base biases. Homologous sequences of the two viroids in the terminal right (TR) region are rich in vd‐sRNAs, and the high frequency vd‐sRNAs selected from the CBCVd TR region can be used to degrade the transcripts of CEVd in vivo directly. These results suggest that RNA silencing may play an important role in the antagonism of the two viroids, thus deepening our understanding of the molecular interaction of long noncoding RNAs in woody plants. [ABSTRACT FROM AUTHOR]