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The bacteria pathogen <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> (<i>Xoo</i>) infects rice and causes the severe disease of rice bacteria blight. As the central regulator of the salic acid (SA) signaling pathway, NPR1 is responsible for sensing SA and inducing the expression of pathogen-related (PR) genes in plants. Overexpression of <i>OsNPR1</i> significantly increases rice resistance to <i>Xoo</i>. Although some downstream rice genes were found to be regulated by <i>OsNPR1</i>, how <i>OsNPR1</i> affects the interaction of rice-<i>Xoo</i> and alters <i>Xoo</i> gene expression remains unknown. In this study, we challenged the wild-type and <i>OsNPR1-OE</i> rice materials with <i>Xoo</i> and performed dual RNA-seq analyses for the rice and <i>Xoo</i> genomes simultaneously. In <i>Xoo</i>-infected <i>OsNPR1-OE</i> plants, rice genes involved in cell wall biosynthesis and SA signaling pathways, as well as PR genes and nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes, were significantly upregulated compared to rice variety TP309. On the other hand, <i>Xoo</i> genes involved in energy metabolism, oxidative phosphorylation, biosynthesis of primary and secondary metabolism, and transportation were repressed. Many virulence genes of <i>Xoo</i>, including genes encoding components of type III and other secretion systems, were downregulated by <i>OsNPR1</i> overexpression. Our results suggest that <i>OsNPR1</i> enhances rice resistance to <i>Xoo</i> by bidirectionally regulating gene expression in rice and <i>Xoo</i>.