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Fuchs endothelial corneal dystrophy (FECD) is a bilateral progressive corneal endothelial disease characterized by guttae, which present as partial Descemet membrane thickening, inducing corneal edema at the final stage. Oxidative stress has been reported to play an important role in the pathogenesis of FECD. The electron transport chain and oxidative phosphorylation (oxphos) system in mitochondria are the main sources of endogenous oxidative stress, arising from superoxide generation through premature electron leakage to oxygen. In FECD, corneal endothelial cells have altered mitochondria with mitochondrial DNA damage, decreased oxphos proteins, and lower mitochondrial membrane potential. Mitochondrial dynamics and mitophagy comprise the organelle-level mitochondrial quality control system. Mitochondrial dynamics includes fusion and fission processes. When mitochondria are severely damaged, fission becomes the dominant process to remove damaged mitochondria. Mitophagy is a selective autophagy pathway that removes damaged mitochondria, and is triggered by mitochondrial membrane potential depolarization. In the FECD corneal endothelium, mitochondria have a fission-dominant morphology and low density through mitophagy upregulation because of quality control processes against altered mitochondria.