Abstract: A study of the hair microstructure from the back, the abdomen, the neck, the throat, the hip and the tail of the Tragulus kanchil was conducted by Scanning Electronic Microscope and Polarized Optial Microscope, we selected 7 morphology indices including scales number from the thickest part of hairs, scales number from the lateral per unit length (200 μm) of hairs, length-width ratio of scales from the thickest part of hairs, length-width ratio of scales from the flat scale, the ratio of the irregular wave type to the total length of the hair, the ratio of the flat scale to the total length of the hair and medullary index in order to research the microstructure of the mouse deer’ hair. The result showed that the scale types were mainly irregular wave type and flat type from 6 parts, in which the back and abdomen were mainly flat, and the other 4 were irregular wave type. The medullary was not distinct difference, and the medullary index ranged from 70.1% to 86.1%, the medullary index was not a significant difference among 6 parts, scales number from the thickest part of hairs ranged from 2.47 to 4.28, scales number from the lateral per unit length (200 μm) of hairs ranged from 3.63 to 6.72, length-width ratio of scales from the thickest part of hairs ranged from 0.19 to 0.34, length-width ratio of the flat scale ranged from 0.19 to 0.34. There are more or less differences between the above indicators in the 6 parts. Therefore, we must determine the source of the sample when we identify species by morphological characteristics.