In this study, 107 fecal specimens were collected from 40 sampling sites in Taiwan livestock and avian farms to test for Giardia cysts. Enzyme-linked immunosorbent assay (ELISA) and immunofluorescent microscopic examination were performed as a presumption test and confirmation test, respectively. Eight out of 107 samples analyzed by ELISA showed the presence of Giardia, among which six samples were confirmed by immunofluorescent microscopic examination, and four samples were reconfirmed by polymerase chain reaction method. Giardia species were identified by nucleic acid sequencing method of beta-giardin gene. Two Giardia duodenalis assemblage A isolates and E isolates were all detected from cattle feces. This is the first identification of genotypes of G. duodenalis in the feces of feeding animals in Taiwan.