Objective Morphological observation and gene analysis identification to the strain of flagellate in tree shrews.Methods The tree shrews ileocecal contents and feces by filtering centrifugal were observed microscopically direct smear and iodine staining, the total DNA extracted by the traditional method, the 18S rRNA of flagellate was amplified by PCR, then sequenced. Taking homology analysis by the BLAST, and developing the phylogenetic tree using MEGA5.1.Results Morphological observation showed that flagellate in tree shrews was tritrichomonas. Sequencing analysis indicated that homology of 18s ribosomal RNA between tree shrews giardia and the reported tritrichomonas fetus 18S ribosomal RNA(AY754332.1) was as high as 99%. Conclusion Tree shrews can affect tritrichomonas fetus and the results provide the basis for parasitology quality control of tree shrews.