Abstract: 【Objective】 To clarify the distribution, taxonomic status, morphological characteristics and genetic differentiation of 16S rRNA of salt cedar witches'-broom disease in southern Xinjiang. 【Methods】 In this study, the distribution and damage of salt cedar witches'-broom(SCWB) disease in southern Xinjiang were investigated and the pathogens of SCWB was observed by transmission electron microscope, 16S rRNA gene and rp gene amplification. Meanwhile, the molecular identification of the gene was carried out to clarify its morphological characteristics and taxonomic status, and the genetic differentiation of the 16S rRNA gene of SCWB in different areas of southern Xinjiang was studied. 【Results】 The average incidence of SCWB in southern Xinjiang was 9.06%, and the average disease index was 5.66. The existence of phytoplasma granules was observed in the phloem tissue of tamarisk branches. Nested PCR of 16S rRNA and rp gene bands with sizes of 1,219 bp and 1,174 bp were obtained respectively. Through homology comparison and phylogenetic tree construction, it was confirmed that the SCWB belonged to the phytoplasma disease, and belonged to the phytoplasma 16SrXXX-A subgroup in terms of taxonomic status; SCWB phytoplasma could be mainly divided into four lines, and the nucleotide similarity of 16S rRNA gene was between 96.5% and 99.8% in southern Xinjiang. 【Conclusion】 In this study, a systematic study of the phytoplasma disease of SCWB is carried out, the taxonomic status of the pathogen, the distribution and damage of the disease in southern Xinjiang are clarified, and the genetic differentiation of its 16S rRNA gene is analyzed. The rp gene i amplified to increase the content of phytoplasma diseases in the 16SrXXX group, which has provided a theoretical basis for the detection and identification of the disease.