Objective To screen out specific microsatellite markers for use in Tupaia belangeri chinensis genetic testing. Methods Firstly to screen about 700 microsatellite loci from whole genome. Secondly to choose about 100 better loci without defect factors. Lastly 46 primers were designed by 33 tree shrew's microsatellite loci obtained from whole genome and other references. Agarose gel electrophoresis and polyacrylamide gel electrophoresis were used for PCR products, and better loci based on electrophoresis results were chosen. Then STR scan was used to select the microsatellite loci combination for genetic testing.Results Twenty-two microsatellite loci were selected with a significant Stutter peak on STR scanning. Comparing the alternative loci and ultimately selected loci, there were two loci available in the five alternative loci of T. glis. The coincidence rate between T. glis and T.b. chinensis was 40%. There were two loci available in the five alternative loci of T. minor, and the coincidence rate between T. minor and T. b. chinensis was 40%. There were two loci available in the three alternative loci of T. belangeri, and the coincidence rate between T. belangeri and T.b. chinensis was about 70%. Conclusions The 22 microsatellite loci screened in this study are well applied for genetic testing of Tupaia belangeri chinensis, therefore, provide a scientific basis for the genetic quality monitoring of tree shrews.