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Magnaporthe oryzae is one of the most destructive pathogens that threaten rice production around the world. Previous studies mainly focus on pathogenic mechanism of M. oryzae during infection on rice at leaf stage. However, the pathogenic mechanism of M. oryzae infection on panicle tissue is not well understood. In the present study, we performed RNA sequencing (RNA-seq) to study gene expression patterns of M. oryzae during infection at leaf stage and at panicle stage, respectively. The differentially expressed genes (DEGs) of M. oryzae in the infected leaf and panicle tissues were analyzed. Gene ontology (GO) enrichment analysis of DEGs revealed that M. oryzae genes involved in the biological processes were different at leaf and panicle stages. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs indicates that genes related to individual and important pathways may function at different infection stages. In particular, CAZymes carbohydrate esterases (CEs), carbohydrate-binding modules (CBMs), and glycoside hydrolases (GHs) may play important roles during M. oryzae infection on rice leaves, while glycosyltransferases (GTs) and GHs may play important roles during infection at rice panicle stage. Further analysis of effectors (BAS3, BAS113, BAS162, MoCDIP4, and MoHEG13) and their homologous genes suggest that they are involved in host defense suppression. Our findings provide insights into understanding the infection mechanisms of M. oryzae for rice leaf blast and panicle blast disease. [ABSTRACT FROM AUTHOR]