This study was conducted to estimate the prevalence of chlamydiosis (Chlamydophila abortus) in aborted ewes and does from 66 flocks in 8 different districts of two provinces, Slemani and Duhok in Kurdistan Region-Iraq from October 2014 to the end of June 2015. Indirect enzyme-linked immunosorbent assay (i-ELISA) was used to analyze the serum samples that were collected from 271 sheep and 97 goats. Giemsa and modified Ziehl-Neelsen (MZN) stains were used for direct staining examination of the liver of aborted fetuses, vaginal swabs, and placentae of aborted sheep and goats. A total of 368 aborted sheep and goats serum samples were screened for the presence of Cp. abortus antibodies. The results show 53 (14.40 %) serum samples were positive for Cp. abortus antibodies using i-ELISA; including 36 (13.04 %) in Slemani and 17 (18.47 %) in Duhok province. The overall prevalence rate of chlamydiosis was 15.50 % in ewes and 11.34 % in goats.The infection rate of Cp. abortus 18.24 % found in ewes, aged ≤two years was higher than in the ewes aged >two years. Conversely, does aged >two years showed a higher infection rate than does aged ≤two years. However, the difference in the rate of infection between the two age groups wasn't statistically significant (P>0.05). The abortion rate was higher in the late stage of pregnancy, compared to the early and mid stages of pregnancy in both animal species. However, the difference was statistically significant (P< 0.05) in ewes only. In all animals, Cp. abortus infection occurred only once and caused abortion in 9.13 % and 6.97 % of sheep and goats, respectively. The intracytoplasmic inclusion bodies of Chlamydia in the placentae of sheep appeared as small, purple-colored bodies when stained by Giemsa stain and as red bodies using MZN staining inside the cytoplasm of the cells.