Using the tert-Butanol RNA extraction protocol, we succeeded, for the first time, in isolating RNA from cocoa organs infected by C. perniciosa. These results have led to new perspectives regarding the understanding, through genomic studies, of the cellular mechanisms of the infection of the cocoa tree by destructive pathogens such as Crinipellis or Phytophthora spp. The collection of ESTs we obtained will provide new data about the physiology of the interaction between Theobroma cacao and C. perniciosa. In the short term, we plan to do a functional analysis of some candidate genes, which can also be used for mapping, to facilitate introgression strategies and to create new varieties resistant to C. perniciosa. These data may also be related to research on gene expression of cocoa challenged with other pathogens, such as Phytophthora spp.