Five hundred and six fresh fecal samples were collected from Lu'an, Fuyang, Suzhou, Chizhou, Wuhu, Chuzhou and Bozhou in Anhui Province, and detected firstly by direct smear microscopy. The microscopy-positive samples were amplified by nested PCR targeting the triosephosphate isomerase (TPI) and glutamate dehydrogenase(GDH) genes. The positive PCR products were sequenced in both directions. The sequences were analyzed by ClustalX 1.81 for sequence alignment and the neighbor-joining trees were constructed by Mega 5.05. Thirty-two out of 506 fecal specimens were diagnosed as Giardia-positive by microscopy with an infection rate of 6.3%. 23 and 16 of the samples were typed as assemblage E by the TPI (530 bp) and GDH (450 bp) genes, respectively. These findings indicated that there was a different distribution of subtypes of assemblage E in different areas. The zoonosis genotypes such as assemblage A or B was not found in the present study.