Chlamydia abortus is one of the most common abortive agents worldwide in sheep. Few studies have been reported C. abortus infection among sheep in Egypt but the available data is scarce. The objective of the present study was to determine the seroprevalence of C. abortus among sheep, the associated risk factors and its molecular characterization. The present study was conducted on 675 sheep in six Governorates at Northern Egypt. Data analysis confirmed the presence of antibodies against C. abortus in 93 out of 675 sheep. The logistic regression model was fitted to identify the associated risk factors with C. abortus infection. The results revealed that C. abortus increased significantly in ewes (OR = 4.04, 95 %CI: 1.44−11.28) during autumn season (OR = 3.6, 95 %CI: 1.64–8.28), in ewes with a history of abortion (OR = 1.4, 95 %CI: 0.87–2.50) and in farm where no lambing pen (OR = 2.2, 95 %CI: 1.30–3.94) or abscence of post abortion measures (OR = 1.96, 95%CI: 1.23-3.12). In addition, age, flock size and exchange of breeding ram had no significant effect on prevalence of chlamydiosis. Also, PCR assay was confirmed presence of C. abortus as accusative pathogen in aborted ewe and the genetic characterization of Egyptian C. abortus strain revealed 100 % identity with another strain from Iraq. A control program should be applied to reduce economic losses and risk of human infection