During the process of socket healing after tooth extraction, osteoblasts appear in the tooth socket and form alveolar bone;​ however, the source of these osteoblasts is still uncertain. Recently, it has been demonstrated that cells expressing Gli1, a downstream factor of sonic hedgehog signaling, exhibit stem cell properties in the periodontal ligament (PDL). Therefore, in the present study, the differentiation ability of Gli1⁺-PDL cells after tooth extraction was analyzed using Gli1-Cre^ERT2/ROSA26-loxP-stop-loxP-tdTomato (iGli1/Tomato) mice. After the final administration of tamoxifen to iGli1/Tomato mice, Gli1/Tomato⁺ cells were rarely detected in the PDL. One day after the tooth extraction, although inflammatory cells appeared in the tooth socket, Periostin⁺ PDL-like tissues having a few Gli1/Tomato⁺ cells remained near the alveolar bone. Three days after the extraction, the number of Gli1/Tomato⁺ cells increased as evidenced by numerous PCNA⁺ cells in the socket. Some of these Gli1/Tomato⁺ cells expressed BMP4 and Phosphorylated (P)-Smad1/5/8. After seven days, the Osteopontin⁺ bone matrix was formed in the tooth socket apart from the alveolar bone. Many Gli1/Tomato⁺ osteoblasts that were positive for Runx2⁺ were arranged on the surface of the newly formed bone matrix. In the absence of Gli1⁺-PDL cells in Gli1-Cre^ERT2/Rosa26-loxP-stop-loxP-tdDTA (iGli1/DTA) mice, the amount of newly formed bone matrix was significantly reduced in the tooth socket. Therefore, these results collectively suggest that Gli1⁺-PDL cells differentiate into osteoblasts to form the bone matrix in the tooth socket;​ thus, this differentiation might be regulated, at least in part, by bone morphogenetic protein (BMP) signaling.