Induced systemic resistance (ISR) is a mechanism involved in the plant defense response against pathogens. Certain members of theBacillusgenus are able to promote the ISR by maintaining a healthy photosynthetic apparatus, which prepares the plant for future stress situations. The goal of the present study was to analyze the effect of the inoculation ofBacilluson the expression of genes involved in plant responses to pathogens, as a part of the ISR, during the interaction ofCapsicum chinenseinfected with PepGMV. The effects of the inoculation of theBacillusstrains in pepper plants infected with PepGMV were evaluated by observing the accumulation of viral DNA and the visible symptoms of pepper plants during a time-course experiment in greenhouse and in in vitro experiments. The relative expression of the defense genesCcNPR1,CcPR10, andCcCOI1were also evaluated. The results showed that the plants inoculated withBacillus subtilisK47,Bacillus cereusK46, andBacillussp. M9 had a reduction in the PepGMV viral titer, and the symptoms in these plants were less severe compared to the plants infected with PepGMV and non-inoculated withBacillus. Additionally, an increase in the transcript levels ofCcNPR1,CcPR10, andCcCOI1was observed in plants inoculated withBacillusstrains. Our results suggest that the inoculation ofBacillusstrains interferes with the viral replication, through the increase in the transcription of pathogenesis-related genes, which is reflected in a lowered plant symptomatology and an improved yield in the greenhouse, regardless of PepGMV infection status.