The Japanese macaque is an endemic species consisting of two subspecies: Macaca fuscata fuscata (MFF) and Macaca fuscata yakui (MFY). The MFY is indigenous to Yakushima Island and represents a subspecies of MFF that lives from Honshu to Shikoku and Kyushu, Japan. However, the differences in the skulls of the MFY and MFF are unknown, despite these subspecies having different skull sizes. The maxillary sinus (MS) indicates that the features of the frontal view reflect the transversal growth of the maxilla of the skull. In this study, we show the MS structures of the MFF (n = 9, 18 sides) and MFY (n = 10, 20 sides) using a cone-beam computed tomography instrument. Base on three-dimensional (3D) reconstructed images the MS and nasal cavity were found to present almost to no significant differences between MFF and MFY. However, we designated three classifications of the sinus floor based on the 3D MS images of these Japanese macaques: a round-like shape (type a, MFF = 66.7% (12/18), MFY = 45% (9/20)), a flat-like shape (type b, MFF = 22.2% (4/18), MFY = 35% (7/20)), and an irregular shape (type c, MFF = 11.1% (2/18), MFY = 20.0% (4/20)). The sinus floor shapes of the MFF were mostly type a, while those of the MFY were mostly type b. The prevalence of a root contacting the cortical bone is higher in the canine (26.7%, (8/30)) and second premolar (20%, (6/30) of the MFY at the nasal cavity, moreover, this value is higher in the third molar (42.9%, (9/21)) of the MS in the MFY. These results suggest that the features of the floor of the MS are related to the differences in maxillary root apices teeth between MMF and MMF.