Background: The biological control agent Pseudomonas chlororaphis PA23 is effective at protecting Brassica napus (canola) from the necrotrophic fungus Sclerotinia sclerotiorum via direct antagonism. Despite the growing importance of biocontrol bacteria in plant protection from fungal pathogens, little is known about how the host plant responds to bacterial priming on the leaf surface or about changes in gene activity genome-wide in the presence and absence of S. sclerotiorum. Results: PA23 priming of mature canola plants reduced the number of lesion forming petals by 90%. Global RNA sequencing of the host pathogen interface showed a reduction in the number of genes uniquely upregulated in response to S. sclerotiorum by 16-fold when pretreated with PA23. Upstream defense-related gene patterns suggest MAMP-triggered immunity via surface receptors detecting PA23 flagellin and peptidoglycans. Although systemic acquired resistance was induced in all treatment groups, a response centered around a glycerol-3-phosphate (G3P)-mediated pathway was exclusively observed in plants treated with PA23 alone. Activation of these defense mechanisms by PA23 involved mild reactive oxygen species production as well as pronounced thylakoid membrane structures and plastoglobule formation in leaf chloroplasts. Conclusion: Further to the direct antibiosis that it exhibits towards the pathogen S. sclerotiorum, PA23 primes defense responses in the plant through the induction of unique local and systemic defense regulatory networks. This study has shed light on the potential effects of biocontrol agents applied to the plant phyllosphere. Understanding these interactions will aid in the development of biocontrol systems as a viable alternative to chemical pesticides in the protection of important crop systems. Overall design: Mature canola leaf tissue treated with combinations of PA23 or S. sclerotiorum ascospores (3 treatment groups) was compared to a water treated control (all treatments done in triplicate).