In fishes, irrespective of their thermoregulatory capacity or metabolic rate, the main physiological source of reactive oxygen species (ROS) is mitochondria. During active swimming, ROS is by an large provided by red muscle mitochondria. Other tissues such as lens, liver, heart, swimbladder, roe and blood also afford important ROS production and antioxidant levels in resting fish. A close relationship between structure and function is evident in fish mitochondrion with a surface-to-volume optimization by the size of cristae to maximize electron transfer. The mechanism of fish mitochondrial superoxide anion (O₂^•-) and ROS production as well as the mechanism of mitochondrial coupling and proton leak seems similar to that of mammals. Contrary to mammalian red cells, fish erythrocytes possess nuclei and mitochondria. The presence of cardiolipin and the absence of cholesterol in fish mitochondrial membranes confer a high structural flexibility. The difference in phospholipid unsaturation may explain the greater proton leak in endotherms compared to thermoconformers. The present review summarizes our current understanding in respect to comparative aspects of fish mitochondrial function, with an emphasis on the adaptations to changes in temperature, O₂ availability and O₂ consumption, which are generally coupled to changes in antioxidant status and ROS production. Nevertheless, most work on this fascinating area has yet to be done. The literature on the effect of xenobiotics, aquatic contamination, and aquaculture issues are not reviewed. Data on the production of NO and reactive nitrogen species (RNS), on O₂ sensing and on the role of ROS and RNS in cell signalling involving fish mitochondria are almost completely lacking in the literature.