Cryptosporidium is a significant pathogen in humans and animals. Cases of infection by Cryptosporidium parvum, Cryptosporidium meleagridis, and Cryptosporidium baileyi with zoonotic potential have also been reported in domestic birds, and recent studies indicate the presence of new host-adapted species or genotypes in birds. It is generally difficult to discriminate accurately among Cryptosporidium species and genotypes by light microscopy because of the morphological similarity of their oocysts. Although C. parvum and Cryptosporidium hominis are the primary Cryptosporidium species associated with infection in humans, recent studies have shown C. meleagridis to be a significant cause of cryptosporidiosis in both immunocompetent and immunocompromised individuals. Moreover, genetic variation among C. meleagridis isolates from humans and birds has been reported. Therefore, accurate identification of Cryptosporidium parasites using molecular methodologies is important to assess genetic diversity and to elucidate the transmission dynamics of Cryptosporidium parasites. In Japan, the cockatiel is a popular companion sold in many pet shops, but to the best of our knowledge only 11 Cryptosporidium isolates from cockatiels have been identified molecularly. In the present study, we identified five isolates from cockatiels by multilocus (18S ribosomal RNA, actin, Cryptosporidium oocyst wall protein, 70-kDa heat shock protein, and 60-kDa glycoprotein precursor) sequence and phylogenetic analyses. Analyses identified three new genotypes in C. meleagridis, avian genotype III, and a new avian genotype V.