The mesenchymal stem cell (MSC) is a type of tissue stem cell. In clinical studies, cultured MSCs have shown important therapeutic effects on diseases via both the reduction of neurological defects and the regulation of immune responses. However, in vivo MSC localization, function, and properties are poorly understood; therefore, the molecular understanding of MSC hierarchy is less advanced compared to hematopoietic stem cell hierarchy. Runt-related transcription factor 2 (Runx2) is an essential transcriptional regulator of osteoblast differentiation from MSCs. Runx2 deficiency in Paired-related homeobox 1 (Prrxl)-derived cells (Runx2(prrx1)(-/-)mice) results in defective intramembranous ossification. Double-positive cells for Prrxl-GFP, and stem cell antigen-1 (Scal) (Prrxl +Scal cells) in the calvaria, express Runx2 at lower levels, and are more homogeneous and primitive compared with Prrxl +Seal- cells. Our results suggest that osteoblast differentiation in vivo may begin at the Prrxl 'Scal MSC stage, with sequential progression to Prrxl +Scal- cells, followed by Osterix+Prrx1-Scal osteoblast precursors, which eventually form mature al (I)-collagen+ osteoblasts. This research will enable us to better understand the in vivo molecular biology features of MSCs, leading to their therapeutic applications for tissue repair and regeneration.