Abstract: A study of the microstructure of hair’s from the head, the neck, back, the abdomen and the hip of Muntiacus crinifrons was conducted by scanning electronic microscope and polarized optial microscope, we selected 6 morphology indices including medullary index, the ratio of the different scales type to the total length of the hair, length and width of scales from the thickest part of hairs, length-width ratio of scales from the thickest part of hairs and scales number from the thickest part of hairs in order to research the microstructure of the black muntjac’ hair. The results showed that the medullary was not distinct difference, and the medullary index ranged from 69.1% to 93.8%, the medullary index was a significant difference among 5 parts except for between the abdomen and the hip. The dominant scale pattern in different parts of black muntjac were irregular wave type and flat type, and the proportion of the irregular wave type was 86.7% from the head, another parts were all below 30%. The length and width of scales from the thickest part of hairs ranged from 31.33 μm to 56.52 μm, the width of scales from the thickest part of hairs ranged from 7.56 μm to 12.91 μm, the length-width ratio of scales from the thickest part of hairs ranged from 0.14 to 0.28, the scales number from the thickest part of hairs ranged from 6.10 to 9.72, there were significant differences in 4 morphology indices between 2 parts except for the width between neck and back, the ratio of length-width between head and abdomen, the number of scales between abdomen and hip. Therefore, we must determine the source of the sample when we identify species by morphological characteristics.