Abstract Background: Coccidiosis in birds, including ostriches, is a major concern for animal health and productivity worldwide. There is limited data on Eimeria infections in farmed ostriches (Struthio camelus). Therefore, this research aims to investigate the species of Eimeria in ostriches using molecular methods. It is considered the first detailed molecular study of Eimeria species in Iraqi ostrich farms. Methods: A total of 150 ostrich feces samples from farms in three regions of Iraq using both microscopy and molecular methods. Statistical analysis of the positive samples was performed using the chi-square test, with the significance level set at a p-value < 0.05. Results: Initial testing showed a high prevalence rate of 51.33%. Five samples, out of a total of 77 suspected cases, underwent polymerase chain reaction (PCR) for confirmation followed by sequencing of the 18S rRNA gene. Sequencing results revealed two species of Eimeria: E. praecox and E. tenella. Notably, this is the first report of E. tenella infection in Iraqi ostriches. Genetic analysis of their sequences was performed and deposited in GenBank under accessions NO PV078121.1 to PV078125.1). Conclusions: These results have important implications, including understanding the host specificity of Eimeria and the parasite's transmission between other hosts. They also contribute to identifying coccidiosis control strategies in Iraqi ostrich farms. Furthermore, our molecular findings provide a foundation for future comparative research on the epidemiology of Eimeria in birds.