Abstract: Canonical correlation analysis (CCA) was applied to assess the relationship of rhizosphere and non-rhizosphere microorganisms of flue-cured tobacco plants. The results indicated that (1) the population of bacteria was positively correlated with those of ammonifying bacteria in rhizosphere soil. On the other hand, in non-rhizosphere soil, in addition of ammonifying bacteria, the population of bacteria was also positively correlated with nitrite bacteria and aerobic cellulose decomposing bacteria. (2) The populations of bacterial and actinomycete in tobacco plant rhizosphere could be predicted by the populations of bacterial in non-rhizosphere soil, whereas the population of fungi in rhizosphere was not closely linked to those in non-rhizosphere. (3) The populations of ammonifying and aerobic cellulose decomposing bacteria in rhizosphere were significantly positive correlated with those in non-rhizosphere. However, the populations of aerobic nitrogen fixing bacteria, nitrite and nitrifying bacteria, and kalium solubilizing bacteria in non- rhizosphere were not in close association with those in rhizosphere. In conclusion, there is a strong relationship between three microbial groups and six microbial physiological groups as well as between tobacco rhizosphere and non-rhizosphere soil microbe. The relationship between microbial flora in tobacco rhizosphere is different from non-rhizosphere soil.