Coccidiosis is a disease of high economic importance caused by Eimeria species that show ubiquitous distribution among several species including small ruminants. The prevalence of Eimeria infection in sheep and goats in Geneffe village, Suez Governorate, Egypt was determined during the period from March 2015 to February 2016. Total of 277 animals (142 sheep and 135 goats) were clinically examined and fecal samples were collected and tested both microscopically and by PCR. Sera samples of sheep and goats under 1 year were collected for biochemical analysis. Results revealed that (60%) of goats and (57.70%) of sheep were suffering from subclinical coccidiosis. Adult female goats were significantly (P < 0.05) more infected (82.2%) than adult male goats (40%). Eimeria infection was significantly prevalent in summer (75%) and autumn (74.2%) in sheep than winter (38.2%) and spring (43.2%), while goats did not show significant seasonal variations of infection. The Eimeria species were identified as E. crandallis, E. granulosa, E. ovina, E. parva, E. faurei, E. ovinoidalis, E intricate, E. pallida, E. arloingi, and E. ahasta in sheep, and E. ninakohlyakimovae, E. hirci, E. caprina, E. christenseni, E. jolchijevi, E. apsheronica and E. arloingi in goats. Although animals were subclinically infected with coccidia, some significant biochemical changes were observed in serum samples of sheep and goats. The molecular detection of Eimeria oocysts did not yield any positive results but after sporulation, Eimeria oocysts were detected at zone 100 bp. Our results showed a moderate prevalence of Eimeria infection among adult and yearling sheep and goats in Geneffe village. Suez governorate, Egypt.Hence, good control and prevention programs are necessary.