This study determined the prevalence of Cryptosporidium spp. oocysts in faecal samples from elephant (Loxodonta africana), buffalo (Syncerus caffer) and impala (Aepyceros melampus) in the Kruger National Park (KNP) and an adjacent game reserve in South Africa. Two of the study areas were in close proximity to rural communities on the western KNP boundary and the third study area was located in the centre of the KNP. Fresh stool samples (n = 445) were collected and tested using an immunofluorescent antibody test (IFA) for Cryptosporidium parvum. A total of 278 of these were randomly selected (approximately 90 samples per wildlife species) and tested with the modified Ziehl Neelsen staining technique (ZN) for Cryptosporidium spp. The prevalence of Cryptosporidium spp. was highest in elephants (25.8% [95% confidence interval: 17.3, 35.9]), compared to buffalo (5.5% [1.8, 12.4]) and impala (4.3% [1.2, 10.5]). C. parvum showed similar patterns, being most prevalent in elephants (4.2% [1.5, 8.8]), compared to buffalo (1.4% [0.2, 5.1]) and impala (1.9% [0.4, 5.3]). 29 samples, including ZN positive and IFA positive samples, were retested using a real time PCR (rtPCR) technique. Of the 28 ZN-positive samples, 14 (50%) were positive with rtPCR and of the 9 IFA-positive samples 6 (67%) were confirmed positive by rtPCR. The prevalence of Cryptosporidium oocysts was significantly higher in both of the two study areas adjacent to the western KNP boundary compared to the area in the centre of the KNP (OR = 3.2 [1.2, 9.0]; P = 0.024). Our study demonstrates for the first time the presence of Cryptosporidium spp. in wildlife in South Africa. The transmission of this parasite between wildlife, domestic animals and humans is a plausible hypothesis and represents a potential risk for immunodeficient human populations.