Anaplasma phagocytophilum is a zoonotic pathogen transmitted by arthropod vectors. The pathogen infects various vertebrate hosts, causing mild to severe illness. Molecular studies have demonstrated that A. phagocytophilum exhibits a high level of genetic diversity, with two A. phagocytophilum-related variants identified in several countries. This study represents the first application of PCR amplification and restriction fragment length polymorphism (PCR-RFLP) in conjunction with DNA sequencing to investigate the frequency and phylogenetic relationships of A. phagocytophilum and its related strains in cattle from China. A total of 662 bovine blood samples were collected from diverse regions within Henan Province, China, and pathogen DNA was detected in 75 samples, comprising 11.33% of the total. PCR-RFLP analysis identified three strains with frequency rates of 2.87% (19/662) for A. phagocytophilum, 11.33% (75/662) for A. phagocytophilum-like 1, and 3.22% (22/662) for A. phagocytophilum-like 2. Additionally, co-infections involving A. phagocytophilum and A. phagocytophilum-like 1 were observed as well as between A. phagocytophilum-like 1 and A. phagocytophilum-like 2. Anaplasma phagocytophilum-like strains 1 and 2 should be considered when diagnosing bovine anaplasmosis. Despite recent molecular studies of A. phagocytophilum-related strains, there remains a shortage of data concerning vector capability, the epidemiology of the disease, clinical signs, and genetic diversity of the pathogens. Thus, large-scale investigations involving animals and tick vectors are necessary to obtain more detailed information concerning the etiology of anaplasmosis.