Coccidiosis, caused by species of the apicomplexan parasite Eimeria, is a major disease of pigeons and to quails. Therefore, the present study was conducted to detect the prevalence and identify the species of Eimeria causing coccidiosis in both pigeons and quails in Qena province, Southern Egypt. In the current study, three hundred and sixty fecal samples of each species were collected and screened for Eimeria infection by floatation technique from November 2017 to October 2018.The results of the current study revealed an overall prevalence of 56%, with a higher infection rate in pigeon (58.3%) in comparison to quails (53.9%). Additionally, squabs had the highest prevalence (72.8%) as compared to adults (37.3), whereas the higher prevalence of Eimeria was observed in male birds in both species. Peak prevalence was observed in Autumn and Winter for pigeon and quails respectively. The results also, showed that more than one Eimeria species existed in most fecal samples, and the infection rate of identified Eimeria spp. in these samples was Eimeria labbeana (37.2%), E. columbae (30.8%), E. columbarum (27.9%) and E. gourai (4%) respectively.On the other hand, common Eimeria spp. found in quails were E. tsunoda (51.3%), E. uzura (28%)and E. bateri (20.5%).This indicates that Eimeriatsunoda are the predominant species in Qena Province. Histopathology also revealed a developmental stage of the parasite in the intestinal tract and desquamation of the epithelial lining with areas of necrosis. In conclusion, this study provides basic information on the first detection of coccidiosis of pigeons and quails in Qena Province, Egypt, which has an implication on the sustainable birds' production for human protein requirement.