Bacillus subtilis (B. subtilis) and Pseudomonas fluorescens (P. fluorescens) are two of the most important plant growth promoting rhizobacteria (PGPR) in agriculture. An in situ trial was conducted on greenhouse tomato (Lycopersicum esculentum Mill.) to examine the effect of two bacterial strains, Bacillus subtilis (CGMCC 1.3343) and Pseudomonas fluorescens (CGMCC 1.1802), on tomato growth, gray mold disease control, catabolic and genetic microbial features of indigenous rhizosphere bacteria under lownitrogen conditions. A commercial inoculant (ETS) was also tested as a comparison. Both B. subtilis and P. fluorescens promoted growth and biomass of seedlings, while only B. subtilis was efficient in reducing gray mold incidence in greenhouse tomato. The two bacterial strains could colonization in tomato rhizosphere soil at the end of experiment (10 days after the last inoculation). Different AWCD trends and DGGE patterns were got in different bacterial treatments; however, analyses of microbial diversities showed that indigenous soil microbes did not seem to have significant differences at either the catabolic or genetic level among treatments. ETS, as a commercial microbial agent, promoted plant growth and gave a higher microbial diversity in rhizosphere soil.