Abstract: In order to determine the genetic diversity of Citrus huanglongbing pathogen, 16S rDNA and 16S-23S rDNA intergenic spacer regions of Candidatus Liberibacter asiaticus from 6 different regions were amplified, and the PCR products were analyzed by restriction fragment length polymorphism (RFLP) with 4 restriction enzymes. The electrophoresis bands of digested products of 16S rDNA and 16S-23S rDNA intergenic spacer regions (ISR) were identical and showed no polymorphisms. The 16S-23S rDNA ISR were cloned and sequenced, and the sequences were aligned and analyzed. The results suggested that the 16S-23S rDNA ISR of 6 isolates had no base difference between each other, and the homology level was 99.0% to 100% with other Ca. L. asiaticus. Phylogenetic analysis showed that all Ca. L. asiaticus isolates were clustered into one group, and then clustered in larger group with Ca. L. africanus, Ca. L. americanus and Ca. L. psyllaurous. The results showed that there was no or slight molecular variation of 16S rDNA and 16S-23S rDNA IRS between different isolate of the same specie of citrus huanglongbing pathogen.