Verticillium dahliaewas one of the most important diseases caused Verticillium wilt of cotton. In our previous study,Bacillus axarquiensisTUBP1 was screened and found to be an antagonistic strain againstV. dahliaewith 43% biocontrol effect in the cotton field. In order to uncover the functional mechanism ofB. axarquiensisagainstVerticilliumwilt in cotton, the colonization ofB. axarquiensislabeled with a green fluorescent protein (GFP) was investigated in cotton plants and the rhizosphere soil. Firstly, a plasmid (pHT-315) containinggfpgene was successfully transformed into wildB. axarquiensisTUBP1 and labeled a green fluorescence by electroporation, which didn't change the bioactivity in vitro. In gnotobiotic conditions, cotton seeds were then inoculated with thegfp-labeled strain and grown in green house. Observation with a confocal laser scanning microscope and a scanning electron microscope showed that GFP-labeledB. axarquiensisTUBP1 infected cotton roots and widely distributed in epidermis, cortical parenchyma, intercellular spaces, the xylem vessels, and pith cells as well as root hair cells through cracks formed at the lateral root junctions, followed by a slow migration from roots to stems and leaves. Quantitative fluorescence and flow cytometry (FACS) approaches showed a gradual decrease in the number of TUBP1-315gfpwith increasing inoculation time. However, TUBP1-315gfplevels were detectable till 45 days after planting. In contrast, no fluorescence signal was detected in the non-inoculated groups. Therefore, GFP-labeledB. axarquiensisTUBP1 exhibited colonization in different parts of cotton plants from the rhizosphere soil.