Originating from a benthic ancestor, the suborder Notothenioidei (the dominant fish fauna component of the Antarctic sea) underwent a remarkable radiation, which led notothenioids to fill several niches. The ecological importance of notothenioids in Antarctica and their biochemical adaptations have prompted great efforts to study their physiology and phylogeny, with special attention to the evolutionary adaptation of the oxygen-transport system. We herewith report the evolutionary history of alpha- and beta-globins under the assumption of the molecular clock hypothesis as a basis for reconstructing the phylogenetic relationships among species. These studies have been extended to fish species of other latitudes, including the Arctic region. The northern and southern polar oceans have very different characteristics; indeed, in many respects the Antarctic and Arctic ichthyofaunas are more dissimilar than similar. Our results show that the inferred phylogeny of Arctic and Antarctic globins is different. Taking advantage of the wealth of information collected on structure and function of hemoglobins, we have attempted to investigate the evolutionary history of an important physiological feature in fish, the Root effect. The results suggest that the amino acid residues reported to play a key role in the Root effect may be regarded as ancestor characters, but the lack of this effect in extant species can hardly be associated with the presence of synapomorphies.