Myzus persicae has severe economic impact on pepper (Capsicum) cultivation. We tested two populations of M. persicae, NL and SW (avirulent and virulent) respectively on C. baccatum accession PB2013071. The transcriptomics approach used in the current study, which is the first study to explore the pepper-aphid interaction at the whole genome gene expression level, revealed genes whose expression is differentially regulated in pepper accession PB2013071 upon infestation with these M. persicae populations. The NL population induced ROS production genes, while the SW population induced ROS scavenging genes and repressed ROS production genes. We also found that the SW population can induce the removal of ROS which accumulated in response to pre-infestion with the NL population, and that pre-infestation with the SW population significantly improved the performance of the NL population.