A total of 250 mouse fecal specimens collected from crop farms in Queensland, Australia, were screened for the presence of Cryptosporidium spp. using PCR. Of these, 19 positives were detected and characterized at a number of loci, including the 18S rRNA gene, the acetyl coenzyme A gene, and the actin gene. Sequence and phylogenetic analyses identified two genotypes: mouse genotype I and a novel genotype (mouse genotype II), which is likely to be a valid species. Cryptosporidium parvum, which is zoonotic, was not detected. The results of the study indicate that wild Australian mice that are not in close contact with livestock are probably not an important reservoir of Cryptosporidium infection for humans and other animals.Cryptosporidium sp. is a ubiquitous parasite that is common among wild animals (20). There have been few studies conducted on the epidemiology of Cryptosporidium in wild mice; however, it is important to understand if mice are a reservoir of infection for humans and animals. Studies in different geographical areas have reported prevalence rates ranging from 5.0% to 39.2% in wild rodents, but most have relied on morphology for identification (2)(3)(4)(20)(21)(22).The limited molecular characterization studies that have been conducted on rodents have identified eight species/genotypes: (i) mouse genotype I, which has been identified in mice and rats and in prairie bison in Spain, Portugal, the United Kingdom, Australia, and the United States (1, 16; L. Xiao et al., unpublished data) and to date has not been identified in humans; (ii) the zoonotic Cryptosporidium parvum, which was detected in mice trapped near sheep grazing pastures in Victoria, Australia (16); (iii) Cryptosporidium muris, which infects a range of rodents and is generally not zoonotic but which can infect other hosts, including dogs, hamsters, guinea pigs, chipmunks, rabbits, lambs, cats, and humans (4,9,10,11,18,19); (iv) a novel genotype detected in one wood mouse (Apodemus sylvaticus) sample from the Czech Republic (8); (v) Cryptosporidium meleagridis, isolated from a brown rat (Rattus norvegicus) in Japan (isolate BR5) (13); (vi) eight isolates from brown rats in Japan that clustered with sequences denoted W19 and W19 variants found in New York storm water (12, 13); (vii) three isolates from brown rats in Japan identical to recently described snake isolate 2162 (AY268584) (13, 25); and (viii) another isolate from brown rats in Japan which showed 100% identity with isolates from nonhuman primates in Sri Lanka (EF446679) (5, 13).These studies indicate that the majority of wild mice characterized to date do not carry zoonotic species of Cryptosporidium.