Selected strain of nonpathogenic rhizobacterium EXTN-1 from the Bacillus amyloliquefaciens is capable of eliciting broad-spectrum induced systemic resistance (ISR) in several crops that is phenotypically similar to pathogen-induced systemic acquired resistance (SAR). In tobacco (Nicotiana tabacum cv. Samsun-nn), EXTN-1 treatment also perturbs the disease progress by Pepper mild mottle virus (PMMoV), a member of Tobamovirus group. To investigate the defense mechanisms induced by this rhizobacterium, expression patterns of defense-related genes were analyzed. The EXTN-1-treated tobacco plants showed augmented, rapid transcript accumulation of defense-related genes including PR-1a, phenylalanine ammonia-lyase (PAL), and 3-hydroxy-3-methylglutaryl CoA reductase (HMGR) following inoculation with PMMoV. This was the typical phenomenon of potentiation. Accelerated expression of all these genes was subsequently detected in the noninoculated, upper leaves; thus, their expression is associated with the development of both local and systemic resistance. Coordinated reduction of viral genome accumulation was clearly detected in the leaves of tobacco pretreated with EXTN-1. EXTN-1 treatment on Arabidopsis wild type Col-0 resulted in the activation of PR-1 and PDF1.2 at the same time. All these results may indicated that EXTN-1 induces systemic resistance via salicylic acid- and jasmonic acid-dependent pathways and timely recognition followed by rapid counter attack against the viral invasion is the key differences between incompatible interaction and compatible one.