Assessing gender difference in Japanese Jungle Crows (Corvus macrorhynchos) is difficult by gross observation because both sexes have black plumage colors. Careful observation of the plumage, however, reveals that it is actually iridescent glossy purple and dark-green in color, and that these colors are more marked in adult males than in females. In birds, such iridescent structural colors are generally produced in the feather barbules, where light is scattered constructively by laminar arrays consisting of alternating layers of materials with different refractive indices, namely keratin, melanin and air. We have investigated differences in the microstructure of the feathers of male and female Jungle Crows by means of scanning and transmission electron microscopy. Male birds had more barbs than females, and the length of the prongs was shorter in males than in females. The density of the melanin granules in the cross-section of barbules was higher in males than in females. Moreover, only in males did the melanin granules show an ordered arrangement beneath a keratin cortex layer at the edges of barbules. These results demonstrate that there are microstructural differences in the feathers of male and female Jungle Crows and suggest that the Jungle Crows' feathers may have iridescent coloring that differs according to gender.