Adult stem cells reside in many types of tissues and adult stem cell-based regenerative medicine holds great promise for repair of diseased tissues. Recently, adipose-derived stem cells (ADSCs) were found to be an appealing alternative to bone marrow stem cells (BMSCs) for tissue-engineered bone regeneration. Compared with BMSCs, ADSCs can be easily and abundantly available from adipose tissue. However, our previous study has discovered an important phenomenon that BMSCs have greater osteogenic potential than ADSCs in vitro. In this study, we aimed to explore its mechanism and improve the osteogenic potential of ADSCs for bone tissue regeneration. It has been reported that the epigenetic states could contribute to lineage-specific differentiation of adult stem cells. We observed that the epigenetic changes of BMSCs were much greater compared with ADSCs after a 3-day osteogenic induction. Runt-related transcription factor 2 (Runx2) is essential for osteoblast differentiation and bone formation. We found that BMSCs underwent more obvious epigenetic changes on the Runx2 promoter than ADSCs after osteogenic induction. These results suggest the epigenetic regulation involvement in Runx2 expression, and thus osteogenesis. We subsequently used a histone deacetylase inhibitor, trichostatin A (TSA), to promote the osteogenesis capacity of ADSCs. The results showed that TSA promoted rat ADSCs osteogenic differentiation by altering the epigenetic modifications on the Runx2 promoter in a bone morphogenetic protein signaling-dependent manner.