Small ruminants (sheep and goats) play an important role in the Egyptian economy. Gastrointestinal parasite in sheep and goat caused huge financial losses due to reduction in productivity and health challenges globally. The present study was conducted to determine the prevalence of gastrointestinal parasites in Elbheria and Elmenoufyia governorates. Beside spotlight upon some risk factors that might affect its prevalence. The total prevalence of gastrointestinal parasitic infestation depending on the sedimentation technique is 4.92% and depending on floatation technique is 47.46%. Statistically floatation technique had the ability to detect more infested cases than sedimentation technique. There are eight types of gastrointestinal parasites that had been identified (Eimeria spp., Trichostrongylus spp., Moneizia spp., Ostertagia spp., Haemonchus spp., Strongyloides spp., Trichuris spp., Bonostomum spp., and Balantidium spp.). There are mixed nematodes infestation that had been detected. The prevalence rate within goats (51.66%) was higher than that within sheep examined (46.47%). The female showed higher prevalence rate (ewe 40.856% & doe 58.06) than male (ram 40.29% & buck 41.93%). The animals of age range more than one year and less than 4 years have the highest infestation rate (sheep 59.07% and goat 48.38%). Animals breeds, location, season of the year and rearing system had significant correlation with infestation rates for both sheep and goats. Bahrawy sheep (34.59%) and shamy goats (64.51%) had the highest infestation rates. Ashmon had the highest infestation rate for sheep and goat (33.11%). As well as summer, and large rearing system had the highest infestation rates. Statistically species have no significant correlation with the infestation rate. Similarly, sex of the animal and age of the animal had no significant correlation with the infestation rate. Strict control measures and regular monitoring of the parasitic infestation of the small ruminants' flocks are important to keep them healthy and ensure maximum productivity. Special attention is needed during summer and within large rearing projects to ensure perfect control of gastrointestinal parasites. As well as more attentions should be put in consideration within area has the same demographic nature of Ashmon and when raising bahrawy sheep or shamy goat. Analysis of Egyptian sequences registered in the gene banks revealed that the ITS1 gene is clustered into two clades and the cytochrome c oxidase subunit I (COI) gene is clustered into three clades; Clade one is involved with different Eimeria species in goats from different countries, including Eimeria arloingi and Eimeria hirci in sheep and goats from Ras-Sudr, Egypt, respectively. The second clade involved Eimeria ahsata and Eimeria christenseni in sheep and goat, respectively. The third clade involved Eimeria zuernii in cattle from Egypt.