Abstract: Understanding the mode of action of biocontrol agents plays a key role in the development of novel and effective biofungicides. We propose a transcriptome approach based on dual RNA-Seq to understand, at molecular level, the interaction between biocontrol bacteria and their targeted phytopathogenic fungi and/or oomycetes. This approach was validated on the interaction between the biocontrol bacterium Lysobacter capsici AZ78 and the phytopathogenic oomycete Phytophthora infestans. The RNA-Seq transcriptional profile showed that L. capsici AZ78 cells spread on the mycelium of P. infestans by up-regulating genes involved in biofilm disaggregation and the biogenesis of type 4 pilus. Lysobacter capsici AZ78’s genes involved in antibiotic biosynthesis were up-regulated and they may be linked to the cell death of P. infestans, where putative apoptotic processes were activated and resulted in the down-regulation of primary metabolic pathways. Lysobacter capsici AZ78 cells fed of dead P. infestans mycelium by up-regulating genes encoding lytic enzymes involved in the attack of the main components of oomycete cell walls. Overall, the dual RNA-Seq approach clarified the mode of action of L. capsici AZ78, which is associated with parasitism and predatory activities that cause the death of P. infestans.