Abstract: Nested-PCR detection of Shunchang citrus Huanglongbing pathogen was carried out in this study.Phylogenetic tree based on rDNA sequencing was built to find out the evolutionary between different parts citrus HLB pathogens.Digesting the target DNA fragment of 16S rDNA with restriction enzyme XbaI was carried out to confirm the species of Shunchang Huanglongbing pathogen.The results showed that there were 7 positive detections in 12 selected samples, and the rate of positive detections was 58.33%,and four were dominant character,three were recessive character.The results showed that Shunchang citrus Huanglongbing pathogen belong to Candidatus Liberibacter asiaticus based on the 16S rDNA phylogenetic analysis and restriction enzyme XbaI digestion analysis.And 16S rDNA sequence gap analysis showed that the difference between Ca. L.asiaticus and Ca. L.africanus, Ca. L.africanus and Ca.L.americanus, Ca.L.americanus and Ca.L.asiaticus were 2.75%,3.90%, 3.44%, respectively.