ABSTRACTGenotyping studies on the source and human infection potential ofCryptosporidiumoocysts in water have been almost exclusively conducted in industrialized nations. In this study, 50 source water samples and 30 tap water samples were collected in Shanghai, China, and analyzed by the U.S. Environmental Protection Agency (EPA) Method 1623. To find a cost-effective method to replace the filtration procedure, the water samples were also concentrated by calcium carbonate flocculation (CCF). Of the 50 source water samples, 32% were positive forCryptosporidiumand 18% forGiardiaby Method 1623, whereas 22% were positive forCryptosporidiumand 10% forGiardiaby microscopy of CCF concentrates. When CCF was combined with PCR for detection, the occurrence ofCryptosporidium(28%) was similar to that obtained by Method 1623. Genotyping ofCryptosporidiumin 17 water samples identified the presence ofC. andersoniin 14 water samples,C. suisin 7 water samples,C. baileyiin 2 water samples,C. meleagridisin 1 water sample, andC. hominisin 1 water sample. Therefore, farm animals, especially cattle and pigs, were the major sources of water contamination in Shanghai source water, and most oocysts found in source water in the area were not infectious to humans.Cryptosporidiumoocysts were found in 2 of 30 tap water samples. The combined use of CCF for concentration and PCR for detection and genotyping provides a less expensive alternative to filtration and fluorescence microscopy for accurate assessment ofCryptosporidiumcontamination in water, although the results from this method are semiquantitative.