A novel and sensitive real time PCR was developed to detection Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola, which cause the bacteria leaf blight (BLB) and leaf streak respectively, Universal and specific TaqMan probes, which were designed based on the sequence of Putative siderophore receptor gene cds were used to detect 13 bacteria and one phytoplasmas, only in X. oryzae pv. oryzae and X. oryzae pv. oryzicola, fluorescent signal can be collected with their specific probes respectively. The level of detection of the probe was 30.6fg plasmid, roughly equaling to one cell and 100 times sensitive than PCR gel electrophoresis detection. X. oryzae pv. oryzae and X. oryzae pv oryzicola were detected from seed washes and DNA extracted from the seed washes of naturally infected seeds and infected leaves as small as 10g naturally infected seeds or 0.3g leaf. This method is little time consumption (only 2h) and without contamination from PCR product.