Bovine anaplasmosis caused by the intraerythrocytic rickettsial pathogenAnaplasma marginaleis endemic in South Africa.Anaplasma marginalesubspeciescentralealso infects cattle; however, it causes a milder form of anaplasmosis and is used as a live vaccine againstA. marginale. There has been less interest in the epidemiology ofA. marginalesubsp.centrale, and, as a result, there are few reports detecting natural infections of this organism. When detected in cattle, it is often assumed that it is due to vaccination, and in most cases, it is reported as coinfection withA. marginalewithout characterization of the strain. A total of 380 blood samples from wild ruminant species and cattle collected from biobanks, national parks, and other regions of South Africa were used in duplex real-time PCR assays to simultaneously detectA. marginaleandA. marginalesubsp.centrale.PCR results indicated high occurrence ofA. marginalesubsp.centraleinfections, ranging from 25 to 100% in national parks. Samples positive forA. marginalesubsp.centralewere further characterized using themsp1aSgene, a homolog ofmsp1α ofA. marginale, which contains repeats at the 5′ ends that are useful for genotyping strains. A total of 47 Msp1aS repeats were identified, which corresponded to 32A. marginalesubsp.centralegenotypes detected in cattle, buffalo, and wildebeest. RepeatAnalyzer was used to examine strain diversity. Our results demonstrate a diversity ofA. marginalesubsp.centralestrains from cattle and wildlife hosts from South Africa and indicate the utility ofmsp1aSas a genotypic marker forA. marginalesubsp.centralestrain diversity.