A cross-sectional study was conducted from November 2014 to May 2015 to determine the seroprevalence, assess the presence of active cases through isolation and identify possible risk factors for the MERS-CoV in camels in selected areas of Oromia and Afar regional state of Ethiopia. A total of 472 Dromedary Camel sera were collected and screened with two serological tests: (Pseudoparticle neutralization for screening and Microneutralization test for confirmation. The overall prevalence of MERS-CoV in the study area was (91.5%) (n=432/472). Higher prevalence (92.9%) was recorded in Female Dromedary camel when compared to Male (88.8%) result of multivariate logistic regression shows female camels (OR=2.408) in the study area are 2.4 times at risk of MERS-CoV than male dromedary camel. From Zones included in the study Borena zone recorded the least prevalence (82.2%) (n= 60/73).Multivariate logistic regression shows camels living in Borena zone (OR=0.055) were relatively protected from MERS-CoV when compared to zone 4 of Afar .From the kebeles included camels living in Galifage (OR= 0.018) of Ayssaita district were relatively protected when compared to Urmaytu kebele. Out of 100 swabs collected from four districts (Yabelo, Fentale, Amibara and Dubti) and undergo Real Time PCR , 7 of them evident circulation of MERS-CoV in the study area. Generally this study showed the existence of high seroprevalence of MERS-CoV among Ethiopian dromedary camels and also confirmed with RT-PCR, therefore further study is required to determine its significance from both animal and public health perspectives.