Ischemic heart diseases are a serious health problem worldwide. The transplantation of mesenchymal stem cells (MSCs) has been investigated in numerous clinical trials on various other diseases due to the self-renewal capacity of these cells and their potential to differentiate into a variety of cell types. The presence of excess reactive oxygen species in injured myocardium causes cardiac dysfunction and leads to inefficient repair of the heart. The poor outcomes of stem cell transplantation have been suggested to result from residual oxidative damage affecting the transplanted cells. The aim of the present study was to compare the effects of hydrogen peroxide (H2O2) on Wharton's jelly-derived MSCs (WJ-MSCs) and bone marrow-derived MSCs (BM-MSCs) in vitro, in order to provide information useful for the future selection of MSC types for cardiac differentiation and transplantation. H2O2 at concentrations of 200, 500 and 1,000 µM was applied to WJ-MSCs and BM-MSCs under cardiogenic differentiation conditions. The morphology of MSCs treated with H2O2 was similar to that of untreated cells, whereas the cell density decreased in direct association with the dose of H2O2. Cardiac differentiation markers were then evaluated by immunofluorescence analysis of GATA4 and cardiac troponin T (cTnT). The fluorescence intensity levels of the two markers were identified to be diminished by increasing doses of H2O2 from 500 to 1,000 µM. The expression levels of homeobox protein Nkx2.5, cTnT and cardiac α-actin were also examined, and were identified to be low in the WJ-MSCs treated with 1,000 µM H2O2, which was similar to the findings observed in BM-MSCs. These results suggested that oxidative stress affects cardiomyocyte differentiation via the downregulation of cardiac genes and cardiac proteins. Furthermore, it should be noted that there was a marked difference in the effect depending on the source of MSCs. This evidence provided supportive information for the use of stem cells in transplantation.