Abstract: To clarify the metabolic characteristics of microorganisms in rhizosphere soil, roots and stalks of tobacco plants infected with bacterial wilt and black shank, Biolog-ECO metabolic phenotype technique was used to study the metabolism of 31 carbon sources in six categories for microbial communities. The results showed that: 1)The carbon source metabolic capacities of microorganisms in rhizosphere soil, roots and stalks of the same tobacco plant decreased successively. The utilization rates of carbon sources in six categories by microorganisms in roots and rhizosphere soil did not change significantly after infection, while the utilization rates of polymer, amino acid and phenol carbon sources by stalk microorganisms increased. 2)Microorganisms in roots and rhizosphere soil of tobacco plants infected with bacterial wilt and black shank could metabolize all 31 carbon sources. Stalk microorganisms of tobacco plants infected with bacterial wilt could metabolize 30 carbon sources normally apart from 2-hydroxybenzoic acid. Stalk microorganisms of tobacco plants infected with black shank could not metabolize 10 carbon sources, such as D-mannitol, glucose-1-phosphate, D-glucosaminic acid. 3) The average well color development (AWCD) values of microorganisms in roots and rhizosphere soil of tobacco plants infected with black shank were significantly lower than those of healthy tobacco plants, and the AWCD values of stalk microorganisms were slightly higher than those of healthy tobacco plants. The AWCD values of stalk microorganisms of tobacco plants infected with bacterial wilt were significantly higher than those of healthy tobacco plants, while the AWCD values of root and rhizosphere soil microorganisms were not significantly different from those of healthy tobacco plants. 4)The Shannon-Wiener, Simpson and Pielou indexes of microorganisms in roots and rhizosphere soil of diseased tobacco plants were not significantly different from those of healthy tobacco plants, while the three indexes of stalk microorganisms increased significantly compared to those of healthy tobacco plants.