A 298 bp region of the Cryptosporidium parvum 18S rDNA and a 390 bp region of the acetyl-CoA synthetase gene were sequenced for a range of human and animal isolates of Cryptosporidium from different geographical areas. A distinct genotype is common to isolates from cattle, sheep and goats and also an alpaca from Peru and is referred to here as the ‘calf’-derived Cryptosporidium genotype. Another genotype of ‘human’-derived isolates also appears to be conserved amongst human isolates although humans are also susceptible to infection with the ‘calf’ Cryptosporidium genotype. Mice and pigs carry genetically distinct genotypes of Cryptosporidium. Three snake isolates were also analysed, 2 of which exhibited C. muris genotypes and the third snake isolate carried a distinct ‘mouse’ genotype.