The Macaca fuscata yakui (MFY) is indigenous to Yakushima Island and is a subspecies of Macaca fuscata fuscata (MFF), which lives from Honshu to Shikoku and Kyushu, Japan. However the differences in the skull of the MFY and MFF are unknown, despite the different skull sizes. The infraorbital canal (IOC) indicates that the feature of the frontal view reflects the transversal growth of the maxilla of the skull. In this study, we show the IOC structure of the MFF and MFY using a cone‐beam computed tomography apparatus. These specimens are stored in the osteological collections of the Department of Neurology, Gross Anatomy Section, Kagoshima University Graduate School of Medical and Dental Sciences (Japan). The maximum height of the IOC, the maximum height from the palatine to the inferior border of the center orbital foramen, and the volume of the IOC of the MFF were significantly greater than those of the MFY (p<0.05). We also classified four types of IOC 3D images, a tube‐like shape, funnel shape, pinched shape, and double‐canal type, in these Japanese macaques. However, a double‐canal type separated into two lumens was found in the five cases of MFY (31.3%, 5/16)). These results suggest that the lower face of MFY with a shorter face indicates a need to prepare for a hard diet compared with the MFF and is related to the food preferences between MFF and MYF.