Eimeria spp. infections are one of the most economically significant diseases of sheep and goats. This study aimed to identify Eimeria spp. and its prevalence in sheep and goats reared under the intensive system in Sharkia Governorate, Egypt. Faecal samples (n=125) from sheep (n=64) and goats (n=61) were collected in three main rearing cities. Floatation technique was used to detect the coccidian oocysts in collected samples. Oocysts were allowed to sporulate and then identified based on morphological features and molecular analysis. Prevalence of Eimeria spp. infection was 60.9% in sheep (39/64) and 83.6% (51/61) in goats. Nineteen Eimeria spp. were detected in both sheep and goats. In sheep, ten species (E. ahsata, E. pallida, E. intricata, E. ovinoidalis, E. marsica, E. bakuensis, E. faurei, E. granulosa, E. crandallis and E. parva) were identified with E. ahsata being the most prevalent (26.6%). However, only nine species (E. arloingi, E. alijevi, E. ninakohlyakimovae, E. hirci, E. christenseni, E. aspheronica, E. jolchijevi, E. caprina and E. caprovina) were found in goats and E. arloingi was the most common species (45.5%). Mixed infections with Eimeria spp. were detected in 43.6% (17/39) and 74.5% (38/51) of examined sheep and goats, respectively. The sequence of internal transcribed spacer-1 (ITS-1) region of E. ahsata was 100% similar to ovine E. ahsata, and clustered in a single clade with E. cardinalis and E. faurei. However, E. arloingi was 100% similar to E. arloingi of goat and clustered with bovine E. ellipsoidalis. Our results showed that coccidial infection in sheep and goats reared under intensive production in Sharkia Governorate is high, suggesting that a strategy for controlling the disease is required in Egypt.