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Temporomandibular disorders (TMD) are multifactorial chronic pain conditions involving the temporomandibular joint, masticatory muscles, and associated structures, with a marked predominance in women. Despite their high prevalence and significant impact on quality of life, the biological mechanisms underlying pain chronification in TMD remain incompletely understood. Growing evidence indicates that persistent TMD-related pain arises from complex interactions among inflammatory signaling, oxidative stress, neuroendocrine dysregulation, and epigenetic modulation of gene expression. This integrative narrative review synthesizes current clinical and preclinical evidence from molecular biology, neuroendocrinology, and epigenetics to elucidate the biomolecular mechanisms involved in chronic TMD pain. Studies consistently report elevated proinflammatory cytokines, such as interleukin-6 and tumor necrosis factor-α, alongside increased oxidative stress markers, including malondialdehyde and 8-hydroxy-2′-deoxyguanosine, accompanied by reduced antioxidant capacity in saliva and serum. Alterations in neuroendocrine mediators, particularly dysregulation of the hypothalamic–pituitary–adrenal axis and reduced levels of neurotrophic factors such as brain-derived neurotrophic factor and nerve growth factor, appear to contribute to central sensitization and impaired neuroplasticity. In parallel, epigenetic mechanisms—including DNA methylation of pain- and stress-related genes (e.g.,