We analyzed genetically Cryptosporidium parvum HNJ-1 strain, which is the Japanese reference strain isolated from human in Japan. DNA sequences of genes for thrombospondin-related adhesive protein of Cryptosporidium-1 and Cryptosporidium-2 (TRAP-C1, TRAP-C2), heat shock protein 70 (HSP70), oocyst wall protein (COWP), beta-tubulin, alpha-tubulin, polythreonine-region (Poly-T), elongation factor 1 alpha (EF-1 alpha), and 18S rRNA of this strain were determined. They showed high rate of homology to published sequences of genotype 2 strains, which were considered to be infective to both humans and animals. However, HNJ-1 had synonymous and non-synonymous substitutions in the nucleotide sequence of TRAP-C1 and beta-tubulin among HNJ-1 and published sequences of genotype 2 strains. These results implied that HNJ-1 strain was an unique subpopulation of genotype 2 strain of C. parvum.