Early blight caused by Alternaria solani is a serious threat to crop production. In this study, the synergistic antagonism mechanism of a biocontrol consortium (including Bacillus subtilis J3 and Pseudomonas fluorescens J8) isolated from the tomato rhizosphere against A.solani was investigated. The consortium (10(9) CFU/mL, J3:J8(v/v) = 2:3) efficiently inhibited A.solani growth with an inhibition rate of 94.10%, significantly higher than the single culture of J3 or J8 (P < 0.05). The co-cultivation of J3 and J8 significantly enhanced (6.51-146.81%) the expression of the functional genes related to the production of antimicrobial substances, including srfA, fenA, pvds, phlA, and hcnA. Siderophore and 2,4-diacetylphloroglucinol (2,4-DAPG) were 55.45-70.18% higher in the consortium than in single strains, significantly contributing to pathogen biocontrol. The interchange of metabolic substances between the bacteria probably improved their performance. This paper presents useful biocontrol bacteria material and provides important information on the synergistic mechanism of the bacteria, which could help to design and implement such biocontrol agents.