【Objective】To study the Dynamics in kanamycin-resistant bacterial population and monitor shift of nptII gene in the phyllosphere of insect-resistant transgenic cotton.【Method】Insect-resistant transgenic cotton 33B, SGK321 and GK12,and corresponding receptor cotton 33, Shiyuan 321 and No.3 Simian cotton were sampled at different growing stages. Dynamics and diversity among kanamycin-resistant bacterial populations in the phyllosphere were analyzed with the conventional culture methods. In addition, the shift of nptII gene was monitored by germ PCR, and the unique primer was designed from the sequence of nptII gene, the CK is pBI121 plasmids.【Result】at different sample time,significant differences were found among the total number and diversity index of phyllospere kanamycin-resistant bacterial population each cotton variety, but little differences between Insect-resistant transgenic cotton and corresponding receptor cotton at the same time. we discovered the positive segment from kanamycin-resistant bacteria in the phyllosphere of insect-resistant transgenic cotton SKG321, GK12 and receptor cotton No.3 Simian cotton.【Conclusion】We suggested that little differences were found among the total number and diversity index of phyllospere kanamycin-resistant bacterial population between Insect-resistant transgenic cotton and corresponding receptor cotton,and nptII gene in insect-resistant transgenic cottons could drift into the phyllosphere bacteria.