Melatonin is a multifaceted antioxidant that is unevenly distributed in body fluids and within subcellular organelles. Moreover, melatonin is synthesized in most, if not all, taxa of the animal and plant kingdoms. Fortuitously, melatonin levels seem to be in especially high concentrations in the mitochondria, the major site of reactive oxygen species (ROS) generation. ROS normally inflict extensive molecular damage to mitochondria and other cellular organelles. Melatonin efficiently neutralizes ROS in mitochondria by direct scavenging and indirectly via stimulation of antioxidative enzymes involving a SIRT3/SOD2 signaling pathway as summarized herein; these actions protect this critical energy-producing organelle from malfunction, which would compromise survival of the cell and eventually of the organism.