Abstract Objective: Cardiovascular diseases hold the peak death rate among other illnesses which reveals the significance of current limitations in common therapies. Three-dimensional (3D) scaffolds have been utilized as potential therapies for treating heart failure following myocardial infarction (MI). Methods: In this study, we investigate cardiac differentiation capacity of MenSCs and BMSCs using 5-aza-2′-deoxycytidine(5-aza) and basic-fibroblast growth-factor (bFGF) under 2D and 3D (Bombyx mori silk fibroin scaffold) culture conditions compared to co-culture with neonatal rat cardiomyocytes . The expression of the putative myogenic cells at mRNA and protein levels was determined by immunofluorescent staining and real-time quantitative PCR. Results: Our data revealed that differentiated MenSCs and BMSCs acquired some features of cardiomyocytes, however, degree of differentiation was dependent on the culture conditions. In a similar manner with BMSCs, differentiated MenSCs showed upper levels of mRNA/protein of late stage cardiac markers under 3D culture compared to those induced in 2D and co-culture with neonatal rat cardiomyocytes evidencing the key role of chemical factors and stimulation signal of extracellular matrix in cardiac development of stem cells. Differentiated MenSCs under 3D and co-culture with neonatal rat cardiomyocytes compared to BMSCs showed remarkable expression of Connexin-43,TNNT2 and ACTN-2 at both gene and protein levels, whereas developed MenSCs under 2D culture only expressed connextin-43 and TNNT2 protein at the higher level compared to BMSCs in same conditions. Conclusion: This research demonstrates that MenSCs have relatively higher capability to be differentiated toward cardiomyocyte compared with BMSCs in three conditions. Furthermore, suggests the therapeutic potential of silk scaffold-seeded MenSCs in the treatment of ischemic heart diseases.