Alzheimer's disease (AD) currently underlies dementia for tens of millions of people worldwide, and its occurrence is set to double in the next 20 years. The currently approved drugs for treating AD only marginally ameliorate cognitive deficits, and provide limited symptomatic relief, while newer substances under therapeutic development are potentially years away from benefiting patients. Melatonin (MEL) is a potent antioxidant, can prevent toxic aggregation of Alzheimer's beta-amyloid (Aβ) peptide and, when taken long term, can protect against cognitive deficits in APP transgenic mice. To study the effects of melatonin on brain mitochondrial function in an AD model, APP/PS1 transgenic mice were treated for one-month with melatonin. Analysis of isolated brain mitochondria from mice indicated that melatonin treatment decreased mitochondrial Aβ levels by two to fourfold in different brain regions. This was accompanied by a near complete restoration of mitochondrial respiratory rates, membrane potential, and ATP levels in isolated mitochondria from the hippocampus, cortex, or striatum. When isolated mitochondria from untreated young mice were given melatonin, a slight increase in respiratory rate was observed. No such effect was observed in mitochondria from aged mice. In APP-expressing neuroblastoma cells in culture, mitochondrial function was restored by melatonin or by the structurally related compounds indole-3-propionic acid or AFMK. This restoration was partially blocked by melatonin receptor antagonists indicating melatonin receptor signaling is required for the full effect. Therefore, melatonin receptor signaling may be beneficial for restoring mitochondrial function in AD, and preservation of mitochondrial function may an important mechanism by which long-term melatonin treatment delays cognitive dysfunction in AD mice. However, while melatonin is presumed to provide neuroprotection via activation of the two membrane-bound, G-protein-coupled melatonin receptors (GPCR; MTNRs), some data indicate that MEL acts intracellularly to protect mitochondria and neurons by scavenging reactive oxygen species. Therefore, I sought to determine whether the genetic deletion of the MT1 and MT2 receptors (encoded by the MTNR1a and MTNR1b genes respectively) obviates MEL's neuroprotective actions in the AβPPswe/PSEN1dE9 mouse model of AD (2xAD). Beginning at 4 months of age, both AD and control mice either with or without both MTNR receptors were administered either MEL or vehicle in their drinking water for 12 months. Behavioral and cognitive assessments of 15-month-old AD mice revealed receptor-dependent effects of MEL on spatial learning and memory (Barnes Maze, Morris Water Maze), but receptor-independent neuroprotective actions of MEL on non-spatial cognitive performance (Novel Object Recognition Test). Similarly, hippocampal and frontal cortex amyloid plaque load and serum Aβ1-42 levels were significantly reduced by MEL in a receptor-independent manner, while MEL reduced cortical antioxidant gene expression in a receptor-dependent manner. These findings demonstrate that long-term MEL significantly reduces AD neuropathology and associated cognitive deficits in a manner primarily independent of the two GPCR melatonin cell surface receptors. Furthermore, melatonin receptor activation combined with non-receptor dependent mechanisms provides the clearest benefit, both cognitively and molecularly. Future identification of direct molecular targets for MEL action in the brain should open new vistas for the development of better AD therapeutics.