Paenibacillus polymyxa WLY78 is a nitrogen fixer and it can be potentially applied to biofertilizer in agriculture. In this study, P. polymyxa WLY78 is labelled with gfp gene. The GFP-labelled P. polymyxa WLY78 is used to inoculate wheat, maize and cucumber seedlings grown in the gnotobiotic system and in soil, respectively. Observation by confocal laser scanning microscope reveals that the GFP-labeled bacterial cells are mainly located on the root surface and epidermis of wheat, and only a few cells are present within cortical cells. In maize and cucumber seedlings, bacterial cells were colonized in epidermal and cortical cells, intercellular spaces and vascular system of root, stem and leaf tissue interiors besides on root surfaces. Higher densities of the bacterial cells in roots, stems and leaves indicated that P. polymyxa WLY78 cells could migrate from roots to stems and leaves of maize and cucumber. This study will provide insight into interaction between P. polymyxa WLY78 and host cells.