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Mitochondria are the important organelle of fish cells and they are the energy-generating factory within the cells, providing up to 90% of the energy source in the form of ATP through oxidative phosphorylation. In addition, mitochondria play an important role in program cell death (apoptosis) and necrotic death. Thus, studies on mitochondria are highly significant for our understanding of the growth, development, metabolism, aging, diseases of bio-organisms and biological evolution. Regarding to the studies on mitochondria in fishes, the current studies have mainly focused on utilization of the gene fragments of several mitochondrial DNA (mtDNA)-encoded genes to investigate the different species of fishes and the evolutionary relationships among different species and different populations of fishes.