Abstract: Field experiments were conducted in Shilin and Xundian respectively to study the difference of rhizosphere microbe quantity and functional diversity with plate culture method and Biolog technique among Hongda (high susceptibility, S), Yun87 (middle resistance, MR) and K326 (high resistance, R), three flue-cured tobacco cultivars with different resistance to bacterial wilt and black shank. The results indicated that the amounts of bacteria, actinomycetes and the total number of microbes in tobacco plants’ rhizosphere were positively correlated with the cultivar’s resistance, while it was opposite for the fungi. The consistent tendency was obtained not only at 35 d, 55 d and 75 d after transplanting, but also at two experimental sites. Cultivar and experimental conditions  greatly affected the utilization of six types of carbon source by rhizospheric microbes, as well as the AWCD value. In Xundian site, rhizospheric microbes’ utilization of carbohydrates, amino acids, carboxylic acids, polymers, amines and the AWCD value were all higher at 55 d and 75 d after transplanting for the resistant cultivar than the susceptible one, but it was opposite at 75 d after transplanting for the phenolic acids. In Shilin, significant differences existed among the three cultivars at 35 d, 55 d and 75 d after transplanting for the indices mentioned above, although they were not consistent with cultivars’ resistance. Principal component (PC) analysis even showed that utilization of carbon sources by rhizosphere microorganisms differed significantly among the three cultivars at the two sites, and it was better reflected by PC1 and PC2 at 55 d and 75 d after transplanting, respectively. In conclusion, rhizosphere microbial community structure and functional diversity were greatly affected not only by the cultivars’ difference in resistance, but also by experimental conditions.