Wharton's Jelly mesenchymal stem cells (WJ‐MSCs) are an attractive potential source of multipotent stem cells for bone tissue replacement therapies. However, the molecular mechanisms involved in their osteogenic conversion are poorly understood. Particularly, epigenetic control operating at the promoter regions of the two master regulators of the osteogenic program, RUNX2/P57 and SP7 has not yet been described in WJ‐MSCs. Via quantitative PCR profiling and chromatin immunoprecipitation (ChIP) studies, here we analyze the ability of WJ‐MSCs to engage osteoblast lineage. In undifferentiated WJ‐MSCs, RUNX2/P57 P1, and SP7 promoters are found deprived of significant levels of the histone post‐translational marks that are normally associated with transcriptionally active genes (H3ac, H3K27ac, and H3K4me3). Moreover, the RUNX2 P1 promoter lacks two relevant histone repressive marks (H3K9me3 and H3K27me3). Importantly, RUNX2 P1 promoter is found highly enriched in the H3K4me1 mark, which has been shown recently to mediate gene repression of key regulatory genes. Upon induction of WJ‐MSCs osteogenic differentiation, we found that RUNX2/P57, but not SP7 gene expression is strongly activated, in a process that is accompanied by enrichment of activating histone marks (H3K4me3, H3ac, and H3K27ac) at the P1 promoter region. Histone mark analysis showed that SP7 gene promoter is robustly enriched in epigenetic repressive marks that may explain its poor transcriptional response to osteoblast differentiating media. Together, these results point to critical regulatory steps during epigenetic control of WJ‐MSCs osteogenic lineage commitment that are relevant for future applications in regenerative medicine. J. Cell. Physiol. 232: 2519–2527, 2017. © 2016 Wiley Periodicals, Inc. Wharton's Jelly Mesenchymal Stem Cells (WJ‐MSCs) are an attractive potential source of multipotent cells for tissue replacement therapies. Here, we study the ability of WJ‐MSCs to engage the osteoblast differentiation by analyzing epigenetic signatures at the promoter regions of the two master regulators of this process, RUNX2/P57 and SP7. We find that the RUNX2/p57, but not SP7, gene is expressed in WJ‐MSCs stimulated to differentiate to osteoblasts. This process is accompanied by the enrichment of activating histone marks at the RUNX2‐P57 P1 promoter and maintenance of epigenetic silencing histone marks at the SP7 promoter.