Cryptosporidium spp. are a leading cause of diarrhea in Indian children, but there are no data for prevalent species or subgenotypes. Genetic characterization of Cryptosporidium spp. by PCR-restriction fragment length polymorphism and spatial analysis of cases using Geographical Information Systems technology was carried out for 53 children with cryptosporidial diarrhea in an urban slum. The two most common species were C. hominis (81%) and C. parvum (12%). Other species identified were C. felis and C. parvum (mouse genotype). Five subgenotypes were identified at the Cpgp40/15 locus. Subgenotype Ia predominated among C. hominis isolates, and all C. parvum isolates were subgenotype Ic. C. hominis infection was associated with a greater severity of diarrhea. Sequencing of the Cpgp40/15 alleles of C. felis and C. parvum (mouse genotype) revealed similarities to subgenotype IIa and C. meleagridis, respectively. Space-time analysis revealed two clusters of infection due to C. hominis Ia, with a peak in February 2005. This is the first study to demonstrate space-time clustering of a single subgenotype of C. hominis in a setting where cryptosporidiosis is endemic. Molecular characterization and spatial analysis have the potential to further the understanding of disease and transmission in the community.