Giardia intestinalis is recognized as a significant pathogen in humans and animals, causing diarrhea. Recent molecular studies indicate that G. intestinalis is composed of genetically distinct multiple genotypes. Therefore, it is valuable to distinguish among genotypes in the epidemiology of Giardia infection in humans and animals. Although G. intestinalis has been found in humans and animals in Japan, the genotype of isolates remains unclear except for several isolates from dogs, because identification has been performed only by conventional microscopy. We report herein the genotypes of G. intestinalis isolates distinguished by a phylogenetic analysis. G. intestinalis isolates originated from a patient and a calf were found to have Assemblage B and E, respectively.