Abstract: MyoD is a muscle‐specific transcriptional factor that acts as a master switch for skeletal muscle differentiation. This protein regulates myoblast proliferation and myogenic differentiation and is also a short‐lived regulatory protein that is degraded by the ubiquitin system. However, the lysosomal pathway of MyoD protein degradation remains unknown. In this study, we sought to determine whether melatonin (1, 2 mm)‐induced autophagy causes the degradation of MyoD protein in C2C12 myoblast cells. Melatonin induced a significant increase in expression of the microtubule‐associated protein 1 light chain 3 (LC3)‐II and Beclin‐1 proteins in a dose‐dependent manner. Melatonin treatment also significantly increased p‐ERK, Ras, and p‐Akt expressions in a dose‐dependent manner. However, Bax expression was high compared with the absence of melatonin treatment, and Bcl‐2 expression was high in the 0.1–0.5 mm melatonin treatments and low in the 1 and 2 mm melatonin treatments. Under the same conditions, cytosolic MyoD protein was significantly decreased in a dose‐dependent manner and completely eliminated by 36 hr. This decrease in MyoD protein involved ubiquitin‐mediated proteasomal activity with proteasome inhibitor MG132 or autophagy‐dependent lysosomal degradation with lysosomal inhibitor bafilomycin A1 (Baf‐A1). In the same condition, phosphorylation of the mammalian target of rapamycin, p‐mTOR, and p‐S6K expression with Baf‐A1 or Baf‐A1‐plus melatonin treatment were significantly decreased compared with the levels after treatment with melatonin only. Together, these results suggest that melatonin (1, 2 mm)‐induced autophagy results in partial lysosomal degradation of MyoD protein in C2C12 myoblast cells.