In order to investigate the infection and genotypes of Giardia from different wildlife in Cheng Du zoo, a total of 146 fresh fecal samples were collected and their genome DNA extracted. The β-giardin, tpi and gdh genes were amplified by nested-PCR and the product were sequenced followed by phylogenetic analysis. As a result, two persian fallows (CDZOO1 and CDZOO4), a deer (CDZOO2), a tortoise (CDZOO3), a raccoon (CDZOO5), a meerkat (CDZOO6) were infected with Giardia. Multilocus genotypes (MLGs) identified assemblages AI-1 in CDZOO1 and CDZOO3; CDZ002 was infected with assemblage A in both β-giardin and tpi loci; CDZOO4 was confirmed as assemblage A at the tpi locus; CDZOO5 and CDZOO6 were identified as assemblage D at the β-giardin locus while assemblage A based on the tpi locus. In conclusion, this is the first report of molecular epidemiology of Giardia in Chengdu zoo. Meanwhile, Giardia from a tortoise and persian fallow are analyzed by an MLG technique targeting three genes (β-giardin, tpi, and gdh). Furthermore, assemblage A maintained in wildlife and transmitted between them have a zoonotic potential.