In order to find out the mechanism of how salicylic acid signal recruit soil microorganisms to explain their cooperate resistance to Fusarium wilt disease in watermelon plants. In this experiment, we have examined the soil microbial diversity at three different sampling times after salicylic acid application by metagenomic sequencing using Illumina HiSeq platform. The results showed that the incidence of Watermelon Fusarium Wilt was significantly lower than control group after SA application. Collectively, our results indicated that SA signal may activate the immune signal in watermelon plants by mediating rhizosphere microbial community to cooperate enhancing resistance to disease. Notably, SA signal have highly increased the distribution of resistance genes from GH (Glycoside Hydrolases) and PL (Polysaccharide Lyases) after 3 days post inoculation of FON1, and those corresponding resistance genes may came from Proteobacteria because its highest relative abundance. Therefore, our results suggested that the induced resistant observed in watermelon against Fusarium wilt might be a case of cooperate resistance dependent on salicylic acid signal to recruit soil microorganisms.