Since bone apatite is a carbonate apatite containing carbonate in an apatitic structure, carbonate content may be one of the factors governing the osteoconductivity of apatitic bone substitutes. The aim of this study was to evaluate the effects of carbonate content on the osteoconductivity of apatitic bone substitutes using three commercially available bone substitutes for the reconstruction of alveolar bone defects of a beagle mandible with simultaneous dental implant installation. NEOBONE, Bio‐Oss, and Cytrans that contain 0.1, 5.5, and 12.0 mass% of carbonate, respectively, were used in this study. The amount of newly formed bone in the upper portion of the alveolar bone defect of the beagle's mandible was 0.7, 6.6, and 39.4% at 4 weeks after surgery and 4.7, 39.5, and 75.2% at 12 weeks after surgery for NEOBONE, Bio‐Oss, and Cytrans, respectively. The results indicate that bone‐to‐implant contact ratio was the largest for Cytrans. Additionally, the continuity of the alveolar ridge was restored in the case of Cytrans, whereas the continuity of the alveolar ridge was not sufficient when using NEOBONE and Bio‐Oss. Both Cytrans and Bio‐Oss that have a relatively larger carbonate content in their apatitic structure was resorbed with time. We concluded that carbonate content is one of important factors governing the osteoconductivity of apatitic bone substitutes.