Objective To conduct morphological observation and gene identification of the strain of flagellate isolated from Cricetulus migratorius in the Xinjiang Research Center for Experimental Animals. Methods The ileocecal contents of C. migratorius were microscopically examined on direct smear with Wright-Giemsa staining, and the total RNA isolated from Xinjiang C. migratorius was extracted and 16S rRNA was amplified by PCR, and then sequenced. Furthermore the homology was compared and the phylogenetic tree was developed using MEGA5.22 software. Results Morphological observation indicated that the isolated flagellate was Tritrichomonas muris. The 16S rRNA gene sequence of the Xinjiang C. migratorius isolate shared highly homology with that of other Tritrichomonas. Phylogenetic tree analysis indicated that the 16S rRNA gene of Xinjiang C. migratorius isolate was classified into a subgroup with T. muris 16S rRNA (U85966.1), but was relatively distant relative from other related tritrichomonas. Conclusions The flagellate isolated from Xinjiang C. migratorius is identified to be T. muris by both morphological observation and 16S rRNA gene analysis.