Cryptosporidium is apicomplexan parasite that can infect a wide range of animal species as well as humans causing life-threatening diarrhoea, especially in young hosts. In Egypt, few studies on the molecular characterization of Cryptosporidium have been described in humans, but few data were available in animals has been performed until now. The present study aimed to detect and characterize Cryptosporidium spp. for the first time in 195 faecal specimens from ruminant animals of different sites from the South Sinai Governorate. The study was carried out from October 2020 to October 2021 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 ZN and (49%, 53%, and 39.2%) by nPCR in cattle, goats, and sheep, respectively. Host-species, age, and status of faecal samples were risk factors for cryptosporidiosis, whereas location, sex, and clinical state have no significant difference (p> 0.05). The 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 suggest 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.