The WBD Transcriptome Atlas is a comprehensive database that was developed by the Genomics and Expression Laboratory (Unicamp, Brazil) to support the study of one of the most devastating diseases of Theobroma cacao, witches’ broom disease. This database provides the scientific community with access to valuable gene expression data of both the cacao plant and its fungal pathogen Moniliophthora perniciosa. Version 1.1 includes 45 RNA-seq libraries that cover a wide range of biological conditions, from in vitro cultures of the pathogen to its interaction with cacao. Updates will be made available to continuously expand this resource. This initiative is funded by the São Paulo Research Foundation (Fapesp).