The concentrations of Bacillus thuringensis (Bt) toxin released from root exudation of Bt cotton were measured by an enzyme-linked immunosorbent assay (ELISA), and its impacts on the numbers of culturable functional bacteria in the rhizosphere were determined by cultivation. No Bt toxin was found in the rhizosphere of non-Bt cotton (SHIYUAN321), but varying levels of Bt toxin were present in the rhizosphere of two Bt cotton varieties (NuCOTN99B and SGK321) during the entire growth period. The levels of Bt toxin in the rhizosphere of NuCOTN99B were significantly higher (p<0.05) than those of SGK321 within all sampling dates except on June 17th in the whole growth season. Significant differences (p<0.05) were found in the numbers of the three functional bacteria between SHIYUAN321 and NuCOTN99B within each sampling day from May 27th to October 27th. No significant differences were found in the numbers of functional bacteria among three cultivars after growth season. Fortification of pure Bt toxin into rhizospheric soil did not result in significant changes in the numbers of culturable functional bacteria, except the nitrogen-fixing bacteria when the concentration of Bt toxin was higher than 500 ng/g. The results indicated that Bt toxin was not the direct factor causing decrease of the numbers of bacteria in the rhizosphere, and other factors may be involved.