Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 4 2021 08 11 480 487 EN Fariba Taheri Department of Microbiology, School of Veterinary Medicine, Urmia University, Urmia, West Azerbaijan, Iran Abdulghaffar Ownagh Department of Microbiology, School of Veterinary Medicine, Urmia University, Urmia, West Azerbaijan, Iran Karim Mardani Department of Food Hygiene and Quality Control, School of Veterinary Medicine, Urmia University, Urmia, West Azerbaijan, Iran 2021 01 12 2021 03 04 Background and Objectives: Enzootic abortion in sheep and goats, also called ovine enzootic abortion (OEA) or enzootic abortion of ewes (EAE), is caused by Chlamydia abortus. The disease has a major economic impact as it represents the most important cause of lamb loss in sheep in parts of Europe, North America and Africa. This serious and potentially life-threatening zoonosis can also affect pregnant women after contact with lambing ewes, leading to severe febrile illness in pregnancy and loss of the foetus. Materials and Methods: The present study was conducted to the Phylogenetic and Molecular Analysis based on Genes 16S-rRNA, OmpA and POMP of C. abortus in milk samples collected from sheep and goats in West Azerbaijan province, Iran. During 2018, a total number of 360 milk samples were collected from sheep (n = 180) and goats (n = 180) of different regions of the province. All milk samples were subjected to DNA extraction and examined by PCR. Results: Among 360 milk samples collected from sheep and goats, 31 (8.611%; 95% CI=6.13-11.96) were positive for Chlamydia spp. The helicase, 16S-rRNA and ompA genes were examined and resulted in 8, 31, 31 of positive samples respectively. The accession numbers have been deposited in GenBank (NCBI) (MT367602 and MT367603). Conclusion: Phylogenetic analysis based on the gene of helicase showed that most of the isolates shared similarity > 99.97%. https://ijm.tums.ac.ir/index.php/ijm/article/view/2929 https://ijm.tums.ac.ir/index.php/ijm/article/download/2929/1369