The orientation of biological apatite (BAp) is one of the bone quality parameters dominating bone mechanical function. In the mandible, the preferential orientation of the BAp c-axis changes depending on alteration of the in vivo stress condition induced by a change in the biting stress. In this study, to clarify the functional adaptation of the preferential BAp orientation and bone mineral density (BMD), all beagle mandibular molars on one side were extracted to remove the biting stress, leading to changes in both BAp orientation and BMD. The BMD exhibited discontinuous distribution around the first molar, mainly responsible for mastication, on the normal side. However, the distribution was continuous along the mesiodistal axis of the edentulous side. The preferential BAp orientation was analyzed in mandibular cross-sections at the first molar root region. Molar extraction led to a change in the BAp orientation: immediately under the root region on the lingual sides, two-dimensional preferential alignment in the mesiodistal and biting directions of the normal side changed to one-dimensional alignment along the mesiodistal axis of the edentulous side. One-dimensional alignment was also observed on the buccal sides irrespective of molar extraction. These findings clarify the close relationship between in vivo biting stress and the preferential BAp orientation, and will be useful clinically for diagnosis, implant placement, and so on.