Super enhancers (SEs) are large clusters of transcriptional activity enhancers, which drive and control the expression of cell identity genes, as well as differentiation of specific cell types. SEs have great application potential in pathogenic mechanism studies in developmental biology, cancer, and other diseases. However, the potential function and regulatory mechanism of SEs in the osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) are unknown. Therefore, this study investigated the potential function of SEs in the osteogenic differentiation of hBMSCs and their target genes. Osteogenesis was induced in three hBMSCs groups for 14 days. Further, ChIP-seq was performed on cells before and after osteogenic differentiation. Two target genes were then selected from cells before and after osteogenic differentiation for RT-qPCR. Finally, the selected SE target genes were analyzed by bioinformatics. In total, 1,680 SEs were identified in hBMSCs. After 14 days of osteogenic induction, only 342 SEs were detected in cells, among which 1,380 unique SEs were detected in hBMSCs, 42 unique SEs were found in cells induced by osteoblast differentiation after 14 days, and 300 SEs were common in both groups. Further, 1,680 genes were found to be regulated by SEs in hBMSCs, including 1,094 genes with protein-coding function and 586 noncoding genes. Additionally, 342 genes were regulated by SEs in cells after 14 days of osteogenic differentiation induction, of which 223 and 119 had protein-coding and noncoding functions, respectively. KEGG analysis of SE target genes before and after osteogenic differentiation showed the TGF-β, PI3K-Akt, and ECM receptor signaling pathways as highly enriched and closely related to osteogenic differentiation. Further, RT-qPCR results of four selected target genes confirmed the sequencing results. Taken together, osteogenic differentiation of hBMSCs involves changes in multiple SEs, which may regulate the osteogenic differentiation of hBMSCs by regulating the expression of target genes. Copyright © 2021 Zhijie Huang et al.