Abstract: In this study, 4 types of feathers(facial feather, contour feather, remiges and rectrices) of Bubo bubo and Ketupa flavipes were observed by scanning electron microscopy. The number of ventral teeth, hooked barbules and cilia, the nodular diameter and the distance between nodules from downy were measured and recorded and we analyze the data by SPSS22.0. It provides an important basis for the identification of bird species and is crucial for the detection of cases. The results showed that the indices except for the number of hooked barbules of remiges and rectrices and indices from contour feather were significant differences between B. bubo and K. flavipes, as well as there were significant differences in length of basis nodular and nodular diameter from the downy at the base of contour feather between B. bubo and K. flavipes. Therefore, we can distinguish between B. bubo and K. flavipes by the microstructure of their facial feathers, contour feathers, remiges and rectrices.