Rice bacterial blight (BB) is a worldwide rice disease devastating rice yield seriously. In order to explore new resistance genes against BB, we investigated resistance spectrum of W6023, an introgression line derived from cross between o.rufipogon and cultivated rice. Inoculation assays showed that W6023 was highly resistant to 23 of the 25 Xanthomonas oryzae pv. Oryzae (Xoo) strains tested, and the broad resistance spectrum is different from those conferred by other known BB resistance genes. Subsequently, W6023 and its susceptible recurrent parent IR24 were in?ltrated with the broadly virulent Xoo strain PXO99(P6) and RNA-seq analysis was performed. Totally 105644962 and 91022599 sequences were obtained from W6023 and IR24, respectively. GO annotation and KEGG enrichment analysis revealed differentially expressed genes (DEGs) mainly enriched in biosynthesis of secondary metabolites, plant hormone signal transduction and starch & sucrose metabolism. Among these differentially expressed genes, there were 203 significantly differentially expressed genes, of which 114 genes (56.2%) were up-regulated and 89 (43.8%) down-regulated in W6023, and 35.9% of them were located on chromosome 11. Bioinformatics analysis showed that 16 out of the 203 differentially expressed genes belonged to disease resistance genes such as NBS-LRR or receptor kinases; 14 genes were directly or indirectly associated with metabolism of peroxides in rice, encoding peroxidase, metallothionein, and so on; 6 genes encode resistance-related transcription factors, such as WRKY and NAC; 18 signal transduction-related genes encode calmodulin binding proteins, terpene synthase, glucosyltransferase, and so on. Six up-regulated genes of W6023 and three up-regulated genes of IR24 were randomly selected and analyzed by RT-PCR and qRT-PCR. The results were consistent with the data of transcriptome sequencing, indicating that the transcriptome data obtained in this study were reliable. These above results provide a basis for the further isolation of resistance genes in W6023.