Coccidiosis is widespread and common enteric protozoal disease of rabbits. The current study showed prevalence of Eimeria spp. amongst rabbits was 34.93%. Additionally, eight Eimeria spp. were identified using light microscope; whereas E. coecicola and E. irresidua were more frequent among all Eimeria spp. while, four Eimeria spp. were detected using PCR methods. Further, rabbits with mixed infections (72.55%) of different Eimeria spp. were higher than those with single infections (27.45%). Histopathology also revealed a developmental stages of Eimeria in enterocytes of intestinal villi and desquamation of the epithelial lining the lumen. It can be concluded that the current research provides appropriate data that help for assessing the potential infection and future control measurements against rabbit coccidiosis to mitigate the financial losses in rabbit industry in Egypt.