Objective To investigate the prevalence and molecular characteristics of Anaplasma infections in sheep and goats in Anhui Province in 2020, so as to provide insights into ovine anaplasmosis prevention and control. Methods A total of 355 fresh blood samples were collected from 7 sheep and goat farms in Linquan County of Fuyang City, Lixin County of Bozhou City, Yu'an District of Lu'an City, Wangjiang County of Anqing City, Nanling County of Wuhu City, and Tianchang City and Fengyang County of Chuzhou City in Anhui Province from June to December 2020. A. bovis and A. phagocytophilum 16S ribosomal RNA (16S rRNA) gene, A. ovis major surface protein 4 (MSP4) gene and A. capra citric acid synthase (gltA) gene were amplified using PCR assay in all blood samples, and the prevalence of A. bovis, A. phagocytophilum, A. ovis and A. capra infections was calculated in sheep and goats. In addition, the positive amplification products were sequenced and subjected to genetic evolutionary analysis. Results The overall prevalence of Anaplasma infections was 17.5% (62/355) in sheep and goats in Anhui Province, and the prevalence of A. bovis, A. phagocytophilum, A. ovis and A. capra infections was 2.8% (10/355), 2.5% (9/355), 2.5% (9/355), and 7.0% (25/355), while the prevalence of A. bovis and A. phagocytophilum, A. phagocytophilum and A. ovis, A. phagocytophilum and A. capra and A. bovis, A. phagocytophilum and A. ovis co-infections was 0.8% (3/355), 1.1% (4/355), 0.3% (1/355) and 0.3% (1/355), respectively. No Anaplasma was detected in the sheep and goat farms in Fengyang County, while at least three Anaplasma species were detected in other sheep and goat farms, with co-infections of multiple Anaplasma species identified. The prevalence of Anaplasma infections was 14.7% (24/163) in goats and 19.8% (38/192) in sheep, and the prevalence of Anaplasma infections was 31.0% (31/100) in goats and sheep under 6 months of age, and 12.2% (31/255) in goats and sheep at ages of 6 months and older, respectively. A. bovis, A. phagocytophilum, A. ovis and A. capra were identified in sheep and goats of different breeds and ages. Conclusions Multiple Anaplasma species infections were commonly prevalent in goats and sheep in Anhui Province in 2020, notably A. phagocytophilum, A. ovis and A. capra, which have zoonotic risks. Improved surveillance and prevention and control of Anaplasma infections are required in sheep and goats in Anhui Province.