Coccidiosis is an intestinal parasitic disease of chickens caused by the intracellular parasite Eimeria spp. It is responsible for high rates of mortality and morbidity in the poultry industry worldwide. It has a significant economic impact on poultry production. A cross-sectional study conducted in Soran City/Erbil, Iraq from June 1, 2021, to May 31, 2022, aimed to identify the prevalence, seasonality, and species characterization, of Eimeria spp. using 18S rDNA, and histopathological changes associated with Eimeria infection in Backyard chickens. In total, 400 intestinal scraping and fecal samples were examined, out of which 165 (41.25%) were found to be infected with four species of Eimeria. The highest prevalence of Eimeria was observed in winter at 30.3%, followed by autumn at 29% and spring at 27.2%. The summer season had the lowest number of cases only 13.3%. A morphometric analysis was carried out on sporulated oocysts to determine the species of Eimeria. The analysis detected four species of Eimeria, with decreasing prevalence as follows: Eimeria tenella (25%), E. necatrix (20%), E. acervulina (15%), and E. brunetti (7%). Additionally, mixed infections were found in 33 cases mainly E. tenella + E. necatrix. The amplified gDNA from oocysts using genus-specific primers targeting 18S ribosomal RNA revealed 455 bp gave the genus confirmation. The histopathological study clarified that the invasion of the parasite to the intestinal layer causes damage and necrosis as well as provokes immune responses that were presented by different inflammatory cells and infiltration mainly lymphocytes, plasma cells, and eosinophils.