Giardia duodenalis is a pathogen that has been found in a variety of mammals, including humans, and consists of host-specific (assemblages C, D, E, F, and G) and zoonotic (assemblages A, B) genetic groups. Ferrets are popular pets, and they, like humans, are hosts to this pathogen. The genetic characteristics of the Giardia population in ferrets are unclear because only one ferret isolate has been genotyped. To develop a more complete picture of the genetic characteristics of the Giardia population in domestic ferrets two additional Giardia isolates, recovered independently from two ferrets suffering from intestinal or hepatic giardiasis, were analyzed genetically. The sequences of both isolates at three loci, small subunit ribosomal RNA (SSUrDNA, 292 bp), beta-giardin (734 bp), and glutamate dehydrogenase (GDH, 713 bp) were identical to each other, but the sequences of triosephosphate isomerase locus (TPI, 512 bp) had five substitutions between isolates. Sequence homology and phylogenetic analyses at four loci identified both isolates as members of the assemblage A. Moreover, the sequences of SSUrDNA, beta-giardin, and GDH from both isolates were identical to those of the previous ferret isolate genotyped as assemblage A within the regions of overlap. The result obtained in the present study indicates that at least two genetically different types in assemblage A exist in domestic ferrets. In addition, there have been no reported human and animal isolates with the same sequence as those from ferret isolates at all four loci examined, suggesting that the present ferret isolates might be host-specific.