This study scopes out the incidence, histological and molecular detection of cryptosporidiosisin Clarias gariepinus freshwater fish obtained from the River Nile and drainage canals in Giza Governorate, Egypt. The detection of Cryptosporidium spp. in stomach and intestine scrapings of Clarias gariepinus using the modified Ziehl-Neelsen (mZN) technique; the detection of the anti-Cryptosporidium antibodies in Clarias gariepinus sera using the Enzyme-Linked Immunosorbant Assay (ELISA), histopathological investigation of the stomach and intestine using hematoxylin and eosin (H & E) and molecular identification of isolated Cryptosporidium spp. using Polymerase Chain Reaction (PCR), DNA sequencing and phylogenetic analysis. The monthly prevalence of Cryptosporidium spp. showed the highest infestation rate in July (87.5%) but the lowest in January (44.4%), while the seasonal prevalence revealed the highest infestation rate during summer and the lowest rate in the winter season (51.20%). ELISA showed a higher prevalence of 69.3% than that prevalence obtained by mZN, 64% for the total examined Clarias gariepinus fish. Also, a higher prevalence of Cryptosporidium infection (65.5% and 75.8%) was obtained by ELISA than 61.1% and 68.3% by mZN, in both fish groups from the River Nile and drainage canal, respectively. Concerning histological investigation, the detected Cryptosporidium oocysts were highly homologous to Cryptosporidium spp. oocysts. Concerning the molecular identification of Cryptosporidium spp., PCR analysis revealed the expected positive bands at 1056 bp. DNA sequencing and phylogenetic analysis proved that the isolate Cryptosporidium spp. in the present study was Cryptosporidium molnari. In conclusion, freshwater fishes (Clarias gariepinus) exhibit a high infection rate with Cryptosporidium spp. The drainage canals collected fishes showed a higher prevalence than those collected from the River Nile. This indicates an important public health problem and a potential danger to drainage channels in Egypt. ELISA showed a higher prevalence of cryptosporidiosis than mZN, for the total examined Clarias gariepinus fish and phylogenetic tests proved a novel species of Cryptosporidium molnari.