Cryptosporidium parvum (C. parvum) is recognized as a significant pathogen in humans and animals, primarily as a cause of diarrheal illness. Recent genetic and biological studies indicate that C. parvum is not a single species but composed of genetically distinct multiple genotypes. Thus, it is valuable to distinguish between genotypes in the epidemiology of Cryptosporidium infection in humans and animals. Although C. parvum has been detected in humans and animals in Japan, the genotype of isolates remains unclear because identification has been performed only by conventional microscopy. We report herein the genotypes of C. parvum isolates distinguished by the polymerase chain reaction (PCR)-based diagnostic method. C. parvum isolates, originally obtained from a patient and a pet dog, were found to have cattle and dog genotypes, respectively.