In this study, 107 fecal specimens were collected from 40 sampling sites in Taiwan livestock and avian farms to test for Cryptosporidium spp. oocysts. Ten of 107 samples analyzed by enzyme-linked immunosorbent assay showed the presence of Cryptosporidium spp., among which 6 samples were simultaneously confirmed by immunofluorescence assay and polymerase chain reaction. Nucleic acid sequencing of the 18S rRNA gene identified 3 clusters of Cryptosporidium spp. Three Cryptosporidium parvum isolates were from cattle and sheep feces. One Cryptosporidium andersoni isolate was detected from pig feces. The other 2 novel Cryptosporidium genotypes were not similar to any known Cryptosporidium spp. according to the DNA sequences of the 18S rRNA gene.