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Anaplasma spp. are important zoonotic tick-borne pathogens that impact on human health. There are few reports on the prevalence and molecular genetic characteristics of Cervidae species in China. The purpose of this study, therefore, was to investigate the presence of Anaplasma spp. in blood samples of Tian Shan wapiti (Cervus elaphus songaricus) in the Xinjiang Uygur Autonomous Region of China, and conduct phylogenetic analyses. A total of 50 blood samples (wild deer n = 26, and captive deer n = 24) were collected from the de