Anaplasma phagocytophilum infects a wide variety of wild and domestic animals and causes an emerging zoonotic tick-borne disease. There are no available data regarding the presence of A. phagocytophilum in camels (Camelus dromedarius). Therefore, the objective of this study was to investigate the prevalence of A. pagocytophilum in Iranian camels. Whole blood of 207 camels from five geographical regions of Iran was tested for A. phagocytophilum using polymerase chain reaction (PCR), nested PCR, and specific nested PCR based on 16S rRNA. The overall prevalence of infection in tested animals was 34.2% (71/207). Sex was not identified as a risk factor for A. phagocytophilum infection, but analysis revealed significant differences in age and region. In conclusion, Iranian camels can be potential reservoirs for A. phagocytophilum, and Iran must be considered an enzootic area for this infection as indicated by the high subclinical infection rate in camels.