[Aim] Jujube witches' broom is an destructive disease in the production of jujube (Zizyphus jujuba Mill.). The major objective was to investigate the damage status of jujube witches' broom, associated with phytoplasmas and factors of influence at different jujube growing areas in southern Xinjiang. [Method] A detailed field survey of jujube witches' broom was conducted at different jujube growing areas in Akesu and Kashi regions of southern Xinjiang over four years, and the effects of factors such as planting pattern, management level, jujube variety, planting years and transmission mode on jujube witches' broom were analyzed. [Result] The results showed that jujube witches' broom was spread in a sporadic and clustered way in southern Xinjiang. The wide utilization of grafted seedlings carrying phytoplasmas had spread the disease within orchards and also from diseased areas to disease-free ones. Wild jujube (Z. spinosus Hu) seedlings as important primary sources of the disease, should not be neglected. Differences in field resistance to jujube witches' broom disease were detected. Nested polymerase chain reaction (Nested PCR) and TaqMan probe real-time fluorescent quantitative PCR revealed that there were different proportions of symptomless carrier plants (latent infection) in diseased gardens. [Conclusion] The asymptomatic germ-carrying sapling spread disease by human-caused is the dominant factor in the occurrence and epidemic of this disease in southern Xinjiang.