The malleus is the auditory ossicle, which attaches to the tympanic membrane, and transmits sound to the inner ear via the incus and stapes. Long bones such as femurs and radii are composed of cortical and trabecular bone, bear load and transmit mechanical force. It is unclear to what extent ossicles and long bones share systemic bone metabolism. Here we analyzed these bones in Japanese macaques (Macaca fuscata), primates exhibiting strong seasonality in breeding and non-breeding periods. We hypothesized that bone metabolism changes along with seasonal variations in sex hormone levels in the macaques. We first isolated femurs and auditory ossicles from dried skeletons of macaques that had been collected over the past 30 years. We analyzed bone volume and tissue mineral density (TMD, mg/cm3) using micro-CT assuming that specimens reflected bone volume and mineralization status at time of death. Seasonal variation in females was unclear likely due to small sample size of dried femurs in breeding seasons. In males, however, bone volume of dried femurs show significant seasonality, higher in breeding than non-breeding seasons. TMD of auditory ossicles of male macaques also showed marginal seasonality. We then analyzed radial trabecular and cortical TMD, and serum levels of testosterone and 25-(OH) vitamin D in living macaques in the breeding and non-breeding seasons. These data suggest that both long bones and auditory ossicles exhibit seasonal variation associated with testosterone levels in male Japanese macaques.