Background: Cryptosporidiosis is an emerging zoonotic protozoan disease caused by Cryptosporidium spp. The infection was reported worldwide from domestic animals and humans, including wild animals. From India, no such reports were published on Cryptosporidium infection in captive wildlife. Hence, a pilot study was conducted to report the occurrence of Cryptosporidium infection in captive wildlife of India. Methods: Faecal samples (n=788) were collected from 127 captive wildlife species of three zoological parks viz., Sri Venkateswara Zoological Park (SVZP), Tirupati (n=242); Indira Gandhi Zoological Park (IGZP), Visakhapatnam (n=218); Nehru Zoological Park (NZP), Hyderabad (n=328) and screened for Cryptosporidium infection. Preliminary screening of faecal samples was done for the detection of Cryptosporidium oocysts by modified Ziehl-Neelsen (mZN) staining method and the test positives were confirmed by nested PCR targeting 18S rRNA gene. Nested PCR amplicons were sequenced for determining the Cryptosporidium species. The resultant data were statistically analyzed by Fisher/Chi square, Fisher Exact test using SPSS software v 17.0.Result: In mZN staining method, 7.23 percent of isolates were found to be positive for Cryptosporidium and the highest rate of infection was detected in wildlife at NZP, Hyderabad (8.23%), followed by SVZP, Tirupati (7.44%) and IGZP, Visakhapatnam (5.50%). Cryptosporidium positive faecal samples by mZN staining were further confirmed by nested PCR and positive amplicons were sequenced for determination of Cryptosporidium species. Genetic characterization revealed five species viz., Cryptosporidium parvum; C. ryanae, C. suis, C. muris and Cryptosporidium avian genotype III. The study conclude that, Cryptosporidium infection was prevalent in the captive wildlife from the zoological parks of India and species variation was marked among the wildlife. Based on the available literature, the current study is the first of its kind on the prevalence of Cryptosporidium in captive wildlife from India.