Nitric oxide (NO) is a diatomic free radical compound that as a secondary messenger contributes to cell physiological functions and its variations influence proteins activity and triggering intracellular signaling cascades. Low frequency electromagnetic field (EMF) alters the cell biology such as cell differentiation by targeting the plasma membrane and entering force to the ions and small electrical ligands. The effect of these chemical (NO) and physical (EMF) factors on the expression of the stemness and neuronal differentiation markers in rat bone marrow mesenchymal stem cells (BMSC) was investigated. The cells were treated with low (50 micromolar) and high (1 mM) concentrations of Deta-NO as a NO donor molecule and 50 Hz low frequency EMF. The expression of pluripotency and neuronal differentiation genes and proteins was investigated using real time qPCR and Immunocytochemistry techniques. The simultaneous treatment of EMF with NO (1 mM) led to the down-regulation of stemness markers expression and up-regulation of neuronal differentiation markers expression. Cell proliferation decreased and cell morphology changed which caused the majority of cells obtains neuronal protein markers in their cytoplasm. The decrease in the expression of neuronal differentiation Nestin and DCX markers without any change in the expression of pluripotency Oct4 marker (treated with low concentration of NO) indicates protection of stemness state in these cells. Treatment with NO demonstrated a double behavior. NO low concentration helped the cells protect the stemness state but NO high concentration plus EMF pushed cells into differentiation pathway.