The alteration of supporting structures of the teeth in periodontitis results from the complex interaction between colonies of microorganisms and the immune-inflammatory host response. α-mangosteen contains xanthone which has antioxidant, anti-inflammatory, anti-fungal, and osteoinductive properties and has the potential as an alternative treatment to promote bone remodeling of the damaged bone in periodontitis. This study aims to investigate the effect of α-mangosteen on RUNX2, and TRAP5b. Forty-eight Wistar rats aged 2-3 months with bodyweight 250-300 g were used in this study. Rats were divided randomly into 8 groups (4 groups in 2-day-periods). Group 1 as the negative control, group 2,3, and 4 were given αmangosteen hydrogel with the concentration of 0.5%, 1%, and 2% respectively. The alveolar bone on the left mandible of the rats was removed by using low-speed inverted bur with the size of 3mm in the mesiodistal direction, 2mm in the crown-root direction, and 1mm at the buccolingual direction. The α-mangosteen was applied after on the site of the removed bone in the subject groups. At the end of each treatment period (day 7 and day 14), the examination of RUNX2 and TRAP5b expression with immunohistochemical analysis was done. The results of this study showed that on day 7 and day 14, α-mangosteen had an effect on RUNX2. Meanwhile, the TRAP5b examination showed that there was an effect of α-mangosteen on day 7, but not on day 14. αmangosteen as an antioxidant has a role in bone healing. RUNX2 plays an essential role in osteoblast differentiation, while TRAP5b was found necessary for osteoclast differentiation. The conclusion of this study shows that αmangosteen affect RUNX2 and TRAP5b.