Abstract: Black shank (Phytophora parasitica var. nicotiana) is considered to be the most serious disease which can damage all tobacco cultivars and lead to enormous economic loss in Yunnan tobacco area. Four different resistance cultivars, Yun85 (high resistance, R), K326 (middle resistance, MR), Jingyehuang (middle susceptibility, MS) and Hongda (high susceptibility, S) were selected as experiment materials to study difference of the quantity and diversity of rhizosphere microorganism at different stages and after inoculation by the method of plate culture count and the Biolog method. The purpose of this study was to build good foundation for further studying resistance mechanism of tobacco black shank. The results show that bacterial numbers of different cultivars are first increased and then decreased with the growing process, while fungal numbers are reverse. Meanwhile, the trend inflexions of bacteria and fungi are all happened at the flower budding stage, and that of actinomyces is relatively stable. There are positive correlations between rhizosphere microorganism counts of bacteria and actinomyces and cultivar resistance, and a negative correlation between fungal number and cultivar resistance at the rosette stage and the rapid growing stage. In addition, growth of bacteria is stimulated in rhizosphere environment of the resistance cultivars, while the growth is relatively restrained in the susceptible cultivars. And growths of fungi and actinomyces are promoted in all experiment materials. The analysis results of the Biolog method show that there are some differences in total utilization ability of carbon source and functional diversity in different growth stages of different cultivars, and the average well color development (AWCD), Shannon index and Mclntosh index of the resistance cultivars are more than that of the susceptible cultivars in different growth stages of different cultivars. At the same time, AWCD values and functional diversity of the susceptible cultivars are decreased after inoculating phytophora parasitica var. nicotiana. These results explain that rhizosphere microorganism counts of different resistance cultivars are influenced by its growth and development, and the difference of resistance is mainly showed before the flower budding stage of flue-cured tobacco. At the same time there are significant differences after the inoculation, and the difference and cultivar resistance is closely related.