Citrus melanose is one of the most important diseases in orchards cultivating citrus in the world. Although the disease does not cause yield loss, the profitability of the infected fruits is often reduced in the fresh-market, resulting in economic loss. In this study, disease reduction was proven by pre-treatment with Pseudomonas putida strain THJ609-3. In order to illustrate mechanism of the disease reduction by the bacterial strain, the infection behaviors of Diaporthe citri and necrosis deposit of plant tissue were observed using a fluorescence microscope. On the leaves pre-treated with the strain THJ609-3, germination rates of D. citri conidia were significantly decreased compared to those of the untreated control. Scanning electron microscopical observations showed that bacterial cells were attached to the surface of fungal hyphae. Furthermore, morphological change of germ tubes of the conidia was detected. These results suggest that the disease reduction may be caused by the direct antifungal activity of the bacterial strain on the leaf surfaces.