ABSTRACT: Skeleton system has shown high cell heterogeneousity. Different subpopulation of skeleton stem cells or mesenchymal stem cells have been identified by using varied protein markers. However, the decline of which cell types are responsible for age-related bone loss and what characteristic changes of these cells during aging remain to be determined. In the current study, we constructed a conditional premature aging model by deletion of Zmpste24 (Z24) in different cell types. We found that Prx1Cre; Z24fl/fl mice displayed bone loss while OsxCre; Z24fl/fl mice did not, indicating the populations of Prx1Cre +Osxcre- cells are responsible for age-related bone loss. Using single-cell RNA sequencing, we found two populations exit in Prx1Cre; Ai9+ mice but not in OsxCre; Ai9+ mice. Most strikingly, these two populations were declined in Prx1Cre;Z24fl/fl mice, compared to Prx1Cre;Z24fl/+ mice. The two populations, one is Prx1Cre;CD73+ resident in growth plate, called gpSSCs, responsible for trabecular bone loss. Another is Prx1Cre; Sca1+ resident in periosteum, called pSSCs, responsible cortical bone decrease. More importantly, the naturally aged mice also showed the decrease of these two cell types. By integration of chromatin and transcriptional profiling, we found that these two cell populations displayed increased p53 mediated DNA damage and decreased extracellular matrix (ECM) constituents, supporting the degeneration of two populations during aging. Finally, we found that AgrcCreER Z24fl/fl mice displayed the decrease of trabecular bone, but not cortical bone, consistent with AgrcCreER could only label trabecular bone, but not cortical bone. Overall, our study identified two skeleton stem cells, gpSSCs and pSSCs, which are responsible for the age-related bone loss in trabecular bone and cortical bone, respectively.