Little is known about the prevalence and genotypes of Cryptosporidium in fish. The present study investigated the prevalence of Cryptosporidium species in cultured fingerlings (n=227), wild freshwater (n=227) and wild marine/estuarine species (n=255) of fish in Western Australia by PCR amplification at the 18S rRNA locus. Results revealed a low prevalence of Cryptosporidium infection in fish hosts; 0.8% (6/709). Four species of Cryptosporidium were identified including C. parvum, C. xiaoi and pig genotype II in whiting (Sillago vittata) and a novel Cryptosporidium spp. in mullets (Mugil cephalus). The identification of zoonotic species of Cryptosporidium in fish indicates that future research to gain a better understanding of the public health impacts is warranted. The detection of the protozoa in fish may also be a good sentinel for environmental contamination or ecosystem health.