The quantitative contributions of hemoglobin and myoglobin oxygenation in skeletal muscle depend on physiological factors, especially muscle blood flow (Q( m )) and capillary permeability-surface area (PS). Near-infrared spectroscopy (NIRS) can be used to quantify total heme oxidation, but it is unable to distinguish between hemoglobin and myoglobin. Therefore, a mechanistic computational model has been developed to distinguish the contributions of oxygenated hemoglobin and myoglobin to the total NIRS signal. Model simulations predict how Q( m ) and PS can affect oxygenated hemoglobin and myoglobin.Although both hemoglobin and myoglobin oxygenation decrease with impaired Q( m ), simulations show that myoglobin provides a greater contribution to the overall NIRS signal. A decrease of PS primarily affects myoglobin oxygenation. Based on model simulations, the contribution of myoglobin oxygenation to the total NIRS signal can be significantly different under pathophysiological conditions, such as diabetes and peripheral arterial disorder.