This study was conducted to determine the presence and distribution of Anaplasma ovis and Anaplasma phagocytophilum in small ruminants in Istanbul, Tekirdag, Edirne and Kirklareli provinces in Thrace region of northwestern Turkey during May-September in 2014. A total of 423 blood samples (216 sheep and 207 goats) were collected randomly from small ruminants regardless of the clinical symptoms. Species-specific polymerase chain reaction (PCR) assays, targeting the major surface protein 4 (msp4), were employed for identification of A. ovis and A. phagocytophilum and selected products were confirmed via sequencing. A total of 230 small ruminants (54.37%) were found to be infected with A. ovis and/or A. phagocytophilum. The rates of infected animals for A. ovis and A. phagocytophilum were 50.83% (215/423) and 8.51% (36/423) respectively. Coinfection rate in small ruminants was determined as 4.96% (21/423). Sequence diversity rates of 0-0.94% for A. ovis and 0.41-2.49% for A. phagocytophilum have been observed. This is the first detection of A. ovis and A. phagocytophilum in sheep and goats in Thrace region of northwestern Turkey via polymerase chain reaction and sequence characterization. Further researches are needed to determine the vectors, vector-host interactions and genotypic variants that may affect the presence and distribution of Anaplasma species in the region.