Pasteuria spp. was one of the highly potential biocontrol agents of plant-parasitic nematodes. Based on their 16S rDNA sequences, we developed simple PCR, PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) and PCR-SSCP (polymerase chain reaction-single strand conformation polymorphism) methods for rapid detecting the genetic diversities of Pasteuria spp. in root samples. Using simple PCR, we detected Pasteuria spp. from nine out of thirty nematode-infected samples collected from different crops in Fujian and Guangzhou of China. The genetic diversities of Pasteuria spp. in root samples were examined by PCR-RFLP and PCR-SSCP. Two of the five variant RFLP patterns were predominant among the clones when they were digested by restriction enzyme EcoHI. The results from PCR-SSCP analysis were consistent with those of PCR-RFLP and showed greater gene diversities. Twelve clones were chosen and sequenced. The results indicated the sequences of clones shared 97.8%~99.7% similar identity with those of previously reported P. penetrans, and the clones were further divided into one major clades and seven individual clades in the phylogenetic tree.