Fecal survey by modified Ziehl-Neelsen (MZN) method and immunofluorescence assay (IFA) of Cryptosporidium infection in cattle and goats in Taiwan showed a prevalence of 37.6% (173/460) and 35.8% (44/123), respectively. In addition to the calves, adult cattle were also found to be shedding Cryptosporidium oocyst. No significant difference was observed between diarrheic and non-diarrheic cattle feces with regard to the presence of Cryptosporidium oocyst. Two groups of oocysts with different diameter sizes, possibly indicating two different species, were observed in the cattle feces. By PCR analysis using primers directed against the 18S rRNA gene, followed by sequencing of the amplicon, we were able to confirm that one of the oocyst species belong to that of the bovine genotype of Cryptosporidium parvum. This is the first identification of a genotype of C. parvum oocyst in the feces of cattle in Taiwan.