Abstract:GFP (Green fluorescent protein) is described as one of the important methods to study the interaction between target microbe and host. The shuttle vector pGFP4412, carrying gfpmut3a gene, was transformed into Bacillus subtilis B579 strain and expressed successfully. B579-gfp colonization on the surface of cucumber roots was conducted by combining antibiotics plate recovery and Laser Scanning Confocal Microscope (LSCM). The results showed that GFP-expressing B579-gfp was observed under 488 nm wavelength on the surface of cucumber roots, root bifurcated place and the pileorhiza. The B579-gfp could be recovered by antibiotics plate from three different inoculation ways (seeds soaking dipping roots and pouring roots), the numbers recovered were 4.0?103 , 1.0?104 and 2.0?102 cfu/g, respectively.