Background: Mitochondrial alternative oxidase (AOX) is suggested to be present in mitochondria of most invertebrates but not vertebrates. Independently of the reason concerning the enzyme occurrence in animal mitochondria, expression of AOX in human mitochondria is regarded as a potential therapeutic strategy in treatment of mitochondrial diseases caused by the mitochondrial respiratory chain (MRC) deficiency or blockage. Undoubtedly, development of AOX expression-based therapy requires explanation of AOX contribution to animal physiology. Till now the relevant data has been obtained mainly due to heterologous AOX expression in cells and animals that do not have natively expressed AOX. We think that application of animals natively expressing AOX could importantly contribute to the research and therapy development. Because the available genomic and transcriptomic data suggests the presence of functional AOX protein in mitochondria of the tardigrade Hypsibius exemplaris, we decided to investigate the possibility of the animal application as a model for AOX activity analysis at organismal level.Results: We observed that H. exemplaris tolerance to the blockage of the MRC complexes III and/or IV was diminished in the presence of AOX inhibitor and the inhibitor-sensitive respiration enabled the tardigrade respiration under condition of the blockage. Furthermore, although detection of H. exemplaris AOX at protein level and pronounced oxygraphic registration of its activity required the MRC complex III and/or IV blockage, the obtained data indicated that AOX clearly contributed to the animal functioning, also in the absence of the blockage. Conclusions: According to our best knowledge we demonstrated, for the first time, that AOX activity of small aquatic invertebrates, represented by the studied tardigrade species, can be monitored by measurement of intact specimen whole-body respiration. Furthermore, it was also possible to monitor the impact of the MRC complex IV blockage on AOX expression level and AOX inhibition in the absence of the blockage on animal functioning. Thus, H. exemplaris could be applied as a whole-animal model suitable to study activity and expression regulation of natively expressed animal AOX.