As a fast-growing tree species,paulownia has a wide distribution in China.Paulownia witches-broom is a main disease caused by the phytoplsama belonging to 16SrI-D subgroup in paulownia production.Aiming to investigate the molecular genetic characteristics of paulownia witches-broom phytoplasrna(PaWB)strains from diverse regions in China,and improve the detection and comprehensive management of the disease,total of fifteen PaWB strains from twelve provinces or cities were collected.Six housekeeping genes,including 16S rDNA,dnaK,fusA,rp,secA and tuf,from the fifteen phytoplasma strains were amplified and sequenced.These sequences were analyzed by performing the methods of the multilocus sequence analysis(MLSA)based on nucleotide acid and deduced amino acid sequences.The results showed that there were seventeen polymorphic sites in the six genes and all the strains used in the investigation were divided into three kinds of haplotypes.Haplotype Ⅰ was the dominant haplotype,including thirteen strains,namely PaWB-ahhf,PaWB-bj,PaWB-bjhr,PaWB-gzgy,PaWB-hbbd,PaWB-hncs,PaWB-hnpy,PaWB-jsnj,PaWB-jxnc,PaWB-lndl,PaWB-sdlx,PaWB-sdyz and PaWB-zjtz.The strain PaWB-fjfz from Fuzhou,Fujian province was in a unique haplotype lonely.The MLSA results indicated that PaWB-fjfz had an independent evolutionary branch separating from other fourteen PaWB strains with high bootstrap value.Specific to PaWB-fjfz strain,there were seven nucleotide acid and a deduced amino acid mutation in dnaK gene(glutamic transform to lysine),two nucleotide acid and a deduced amino acid mutation infusA gene(alanine transform to glutamic),a nucleotide acid and a deduced amino acid mutation in tuf gene(asparagine transform to aspartic acid),three nucleotide acid and a deduced amino acid mutation in secA gene(aspartic acid wansform to asparagine),four nucleotide acid and a deduced amino acid mutation in rpL22 gene(threonine transform to alanine),and a deduced threonine deleting in rpL22 gene.Most of the PaWB strains from different areas possessed a comparatively high genetic stability,which possibly related to the ways of the disease spread and relatively lower environmental selection pressure.Besides,the distinctive molecular genetic characteristics demonstrated in the PaWB-fjfz strain suggested that the isolates would be valuable materials for phytoplasma research with respect to the genetic differentiation of the microorganism.