The marine environment confronts its inhabitants with a wide variety of O2 concentrations, as well as with fluctuations of small scale local O2 availability over time. This review analyzes the respiratory response of marine animal ectotherms to fluctuating environmental O2 availability in their specific habitats and reactive O2 species generation under environmental stress, with a special emphasis on temperature. Specifically we compare mitochondrial functioning and reactive O2 species formation in these animals to what is known from endothermal, mammalian species. Among the strategies employed by marine invertebrates to maintain tissue Po2 low and within tolerable margins, the possible role of mitochondrial oxyconformity to control cellular Po2 in water breathers is discussed. Mitochondrial generation of reactive O2 species in ectotherms has been shown to depend on the magnitude of the mitochondrial membrane potential and the mitochondrial H+ leak. Alternative mitochondrial oxidases are described in marine ectotherms and might add to ameliorate reactive O2 species formation. The effect of nitric oxide, which in mammals controls the reduction state of the electron transport by lowering cytochrome-c oxidase O2 affinity remains to be investigated in marine invertebrates. A new concept is proposed, showing how the cross talk of reactive O2 species in metabolically low marine invertebrates could support their outstanding hypoxia tolerance under non-stressed conditions.