Fluorescent silica nanoprobe as a biomarker for detection has attracted much attention in the field of nano-biotechnology recently but no further research applications using fluorescent silica nanoparticles (FSNP) combined with antibody molecules reported to detect pathogen detection. In this study, silica nanoparticles were prepared using the water-in-oil (w/o) microemulsion method. The silica nanoparticles were circular in diameter of 50 ± 4.2 nm. The organic dye, tris-2, 2' -bipyridyl dichlororuthenium (II) hexahydrate (Rubpy), could be incorporated efficiently into the core of silica nanoparticles. The fluorescence of Rubpy-doped silica nanoparticles was photostable using a collisional quenching fluorescence test. The Rubpy-doped silica nanoparticles were conjugated with the secondary antibody of goat anti-rabbit immunoglobulin G (IgG) and successfully detected plant pathogen such as Xanthomonas axonopodis pv. vesicatoria that causes bacterial spot disease in Solanaceae plant. These results demonstrated that the fluorescence silica nanoprobe biomarker will have been potential for rapid diagnosis applications on plant diseases.