Rates of evolution have been important components of many phylogenetic and population genetic studies. In Antarctica, underlying active and abandoned Adélie penguin (Pygoscelis adeliae) rookeries, are well preserved subfossil bones. This thesis aimed to estimate a rate of mitochondria1 (mt) DNA evolution by sampling sequences from serially preserved subfossil bones through time, and compare these to sequences from modern populations. During this study four field expeditions were undertaken in Antarctica during the austral summers, resulting in the collection of over 400 blood and 329 subfossil bone samples. This thesis research showed that the Adélie penguin mtDNA control region is unusually long (1768 b.p.) and contains a repeat complex at the 3'-end. A phylogeny of 17 penguin species (suborder Sphenisciformes) was constructed from rns and rnl mtDNA gene sequences. The characteristics (i.e. heteroplasmy and length variation) of control region sequences from penguin species were plotted onto this phylogeny as a mechanism for investigating their evolution. DNA sequence variation from a total of 381 modern Adélie penguin samples revealed the presence of two distinct maternal lineages (7.1% net sequence difference). One lineage is present in all locations around Antarctica (A) sampled and the other was recorded only in Ross Sea populations (RS). The phylogeographic pattern of the A and RS lineages suggests Adélie penguins were restricted to distinct ice-age refugia during the last glacial cycle. Ancient DNA was extracted from 80 subfossil bones (14C dates ranged from 310-6082 years before present) from 16 locations on the coast of the Ross Sea. The ancient DNA from these frozen subfossil Adélie penguins is extraordinarily well preserved. Using both modern and ancient DNA sequences a rate of mtDNA control region evolution was determined. This estimated rate is five times higher than previous estimates for the avian mtDNA control region. This rate was then used to time the divergence of the two lineages A and RS, and showed they split 83 kyr BP during the last glacial cycle. Adélie penguins appear to have endured dramatic changes to their habitat during the ice-ages of the Late Pleistocene.