To study the sequence characteristic of 16S rDNA from jujube witches′ broom in Anhui Province, we extracted the DNA from healthy and infected leaves from Fanchangchang jujube, cloned 16S rDNA sequence of jujube witches’ broom phytoplasma, and gained a fragment of JWB-FJP1 with 1 248 bp in length. The sequence homology analysis showed that JWB-FJP1 shared the highest identity of 99.92% with Chongqing jujube witches’ broom phytoplasma strain JWB-Xch (JQ675716) and shared the lowest identity of 67.06% with Hebei jujube witches’ broom phytoplasma strain JWB-Hebei(GU184186), and it was classified as a member of 16Sr V-B group. The result indicated that phytoplasma showed different biological characteristic in different areas. This research provided theoretical basis for fast identification and classification of jujube witches’ broom phytoplasma in Anhui local jujube species.