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Summary: Bacillus amyloliquefaciens FZB42 is a type of plant growth‐promoting rhizobacterium (PGPR) which activates induced systemic resistance (ISR) in Arabidopsis. Blocking of the synthesis of cyclic lipopeptides and 2,3‐butanediol by FZB42, which have been demonstrated to be involved in the priming of ISR, results in the abolishment of the plant defence responses. To further clarify the ISR activated by PGPRs at the microRNA (miRNA) level, small RNA (sRNA) libraries from Arabidopsis leaves after root irrigation with FZB42, FZB42ΔsfpΔalsS and control were constructed and sequenced. After fold change selection, promoter analysis and target prediction, miR846‐5p and miR846‐3p from the same precursor were selected as candidate ISR‐associated miRNAs. miR846 belongs to the non‐conserved miRNAs, specifically exists in Arabidopsis and its function in the plant defence response remains unclear. The disease severity of transgenic Arabidopsis overexpressing miR846 (OEmiR846) or knockdown miR846 (STTM846) against Pseudomonas syringae DC3000 suggests that the miR846 expression level in Arabidopsis is negatively correlated with disease resistance. Moreover, miR846 in Arabidopsis Col‐0 is repressed after methyl jasmonate treatment. In addition, jasmonic acid (JA) signalling‐related genes are up‐regulated in STTM846, and the stomatal apertures of STTM846 are also less than those in Arabidopsis Col‐0 after methyl jasmonate treatment. Furthermore, the disease resistance of STTM846 transgenic Arabidopsis against Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) is blocked by the addition of the JA biosynthetic inhibitor diethyldiethiocarbamic acid (DIECA). Taken together, our results suggest that B. amyloliquefaciens FZB42 inoculation suppresses miR846 expression to induce Arabidopsis systemic resistance via a JA‐dependent signalling pathway. [ABSTRACT FROM AUTHOR]