Illumina sequencing technology was used to construct the cDNA library of two Sporisorium scitamineum strains Ss16 (strong pathogenicity) and Ss47 (weak pathogenicity),followed by transcriptome sequencing,and bioinformatics analysis after quality control in order to investigate the differences at transcriptional level between S. scitamineum strains with different pathogenicity and discover pathogenicity-related genes. The results showed that a total of 8.31G（Ss16）and 9.88G（Ss47） clean reads were obtained. There were 649 differentially expressed genes (DEGs) including 299 up-regulated genes and 350 down-regulated genes between Ss16 and Ss47. Results of GO annotation and KEGG pathway enrichment analyses showed that DEGs were significantly enriched in KEGG pathways involved in starch and sucrose metabolism,ABC transporters,degradation of aromatic compounds,metabolic pathways,purine metabolism. These pathways are mostly related to protein biosynthesis,transport and metabolism of substances. It will provide molecular basis for revealing the pathogenic mechanism of S. scitamineum.