Ovine and caprine anaplasmosis is an endemic tick-borne disease in Europe, the Middle East and some African and Asian countries, including Turkey. This study was conducted to determine the prevalence of Anaplasma ovis and Anaplasma phagocytophilum in sheep and goats in the Southeastern Anatolia region of Turkey. For each animal group, 384 individuals were included in the study. Microscopy and Rt-PCR were used to determine the prevalence of anaplasmosis in sheep and goats. Microscopic examination revealed 21.88% (n:84) and 39.58% (n:152) Anaplasma sp. positivity in sheep and goats, respectively. The study revealed that the molecular prevalence values were higher than the microscopic prevalence values for each microorganism. The molecular prevalence of A. ovis was 89.32% (n:343) in sheep and 78.91% (n:303) in goats and the difference was statistically significant (P<0.05). On the other hand, A. phagocytophilum was detected at 42.97% (n:165) in sheep and 15.89% (n:61) in goats. This is the first study in Turkey in which the Rt-PCR method was used for the detection of Anaplasma species in small ruminants. This study demonstrated that Rt-PCR provides more accurate and specific results than microscopic examination. The present study is expected to have contributed in determining the prevalence of Anaplasma species, one of the tick-borne pathogens, in Turkey and provide data on future control strategies for small ruminant anaplasmosis.