In this study, the expressions of pathogenic protein genes (PRs), defence related genes like GR, etc., and signal regulated key genes of SA, JA, ET passway were analyzed through RT-PCR technology in order to understand the mechanism of induced systemic resistance by P. fluorescens PEF-5#18 on tomato. The results showed that the pathogenic Forl and P. fluorescens PEF-5#18 could induce tomato plant resistance by SAR or ISR, respectively, whereas, under the interaction condition of Forl-Tomato- PEF-5#18, the joint-inducing effects from SAR and ISR affected tomato’s resistance. Compared with the control treatment, all of the PRs family (PR1, PR4, PR5, PR6) genes as well as the related defense genes (GR, POX, PAL) were up-regulated, however, the expressing values and dynamic changes of induced genes were influenced by the SAR or ISR type and inducing time. In addition, the results implied the SAR induced by Forl was regulated through SA singal passway, and the ISR induced by P. fluorescens PEF-5#18 was mainly depend on JA or ET singal passway.