The New Zealand Brown teal, Auckland Island teal and Campbell Island teal represent a clade of ducks in various stages between flight and flightlessness. The Brown teal is fully volant, the Auckland Island teal represents the medium stage between volant and flightless and the Campbell Island teal is flightless. Previous studies with different approaches, ranging from comparative morphology over allozyme to several partial mitochondrial DNA datasets, resulted in contradicting phylogenies and therefore the phylogeny remained unclear. Here we present the first whole mtDNA dataset and our results demonstrate that the sub-Antarctic teals Auckland Island teal and Campbell Island teal share a recent common ancestor in the Pleistocene before the last glacial maximum and diverged from their closest relative the Brown teal in the Pleistocene as well. Morphological changes towards flightlessness are also present in the volant Brown teal therefore the change occurred already in the common ancestor of the three species and evolved stronger and faster in the sub-Antarctic teals as an adaption to their environment.