Background: Anaplasmosis due to Anaplasma phagocytophilum is an important tick-borne zoonotic disease, which affects dogs, horses, cattle and human as well. This study aimed to probe the existence of this organism by means of molecular biology techniques for the first time in rural dogs of Khuzestan province, Southwestern Iran. Methods: During Sep 2014 to Apr 2015 blood samples of 103 apparently healthy rural dogs (60 males) were collected for A. phagocytophilum detection by light microscopical examination of Giemsa stained slides and Nested PCR on a fragment of 16S rRNA gene. Results: From the examined slides, 11.65% were positive for A. morulae while 57.28% of infection was revealed by Nested PCR method. There was no statistical difference between ages and sexes of dogs and infection in molecular survey of A. phagocytophilum. Conclusion: Molecular prevalence of A. phagocytophilum was noticeably high. It may cause the incidence of disease in human population.