Cryptosporidium is an apicomplexan parasite that can infect a wide range of animal species as well as humans causing life-threatening diarrhea, especially in young hosts. In Egypt, few studies on the molecular characterization of Cryptosporidium have been described in humans and animals until now. The present study aimed to detect and characterize Cryptosporidium spp. in 195 fecal specimens from ruminant animals of different sites from the South Sinai Governorate for the first time. The study was carried out during the period from October 2020 to October 2021 by microscopic examination using Ziehl-Neelsen fast stain (ZN) and a nested-PCR (nPCR) that targeted the Cryptosporidium oocyst wall protein (COWP) gene. Results showed an overall prevalence rate of infection in 105/195 (53.85%) and 86 /195 (43.59%) using ZN and nPCR, respectively. It was (68.6%, 50%, and 48.2%) by microscopic examination and (49%, 53%, and 39.2%) by nPCR in cattle, goats, and sheep, respectively. Host-species, age, and status of fecal samples were risk factors for cryptosporidiosis, whereas location, sex, and clinical state have no significant difference (p> 0.05). All infections were due to C. parvum, which is dominant in Egyptian isolates preserved in GenBank data, and no correlation between the genotype and the geographic origins. We concluded that the presence of potentially zoonotic species of Cryptosporidium in ruminants in this region suggests that livestock could potentially contribute to human cryptosporidiosis in the study area. Further molecular studies on local human populations are required to understand the transmission dynamics of Cryptosporidium spp. in that region.