Genome sequencing has revealed a rich repertoire of candidate virulence factors in the C. fructicola genome. Lack of data on their expression patterns, however, has limited attempts to prioritize genes for functional validation. In this study, we first compared the global transcriptome profiles of four types of infection-related structures, then examined the expressional changes of SM biosynthetic enzymes, SSPs, CAZYs, and secretory proteases among these structures.