The Pacific rat, Rattus exulans, or Kiore as it is called by Maori, is a small human commensal associated with the human settlement of the Pacific. Archaeological evidence from Island Melanesia connects the distribution of the species with the presumed ancestors of all Polynesians, the so-called Lapita. Excavations have uncovered artefacts unprecedented in the region, comprising a style of distinctively dentate-stamped pottery, fish hooks and animal remains among others. The earliest animal remains are from pigs and R. exulans, which was clearly introduced into this region by the people as part of their cultural complex. On these grounds R. exulans has previously been used as proxy to infer human migration pathways throughout the Pacific. Accessibility of human archaeological material is scarce and by way of proxy a much higher sampling resolution for the commensal allows more specific inferences. While the origin of the Lapita is still widely disputed among disciplines from archaeology over linguistics and genetics, attention is focused on the Bismarck Archipelago, as an essential stepping stone for the distribution of these human migrants into the Pacific. The genetics of R. exulans might contribute to an assessment of the established theories of the Lapita origin. However, to make inferences regarding human migration based on the species, more knowledge is needed about its population structure and distribution history. In this thesis I establish the current population structure of R. exulans by extensive sampling of mitochondrial D-loop sequences across its distributional range with a strong focus on the Bismarck Archipelago. The population is deeply divided into three major geographic regions with more recent regional substructures. With the help of a chronology-based reconstruction of ancestral regional distribution I infer the geographic origin of these observed haplogroups and evaluate the chronology in the light of palaeoclimatic events to distinguish natural dispersal events from those that are human mediated. The marked differentiation of the Philippines and of Remote Oceania is almost certainly connected to a Pleistocene interglacial. And while further differentiation within the Philippines can also be associated with palaeoclimatic events, evidence for dispersal of the species to the east into Near Oceania and the Pacific supports a human-mediated distribution. These results of a dual introduction of lineages into Near and Remote Oceania support a minimum of two separate migration waves of human settlers. One was possibly Lapitaassociated, spreading the Near Oceanic lineage, and a second one passed only tangentially through the Bismarcks but distributed the Remote Oceanic lineage throughout the Pacific. Two competing theories for the origin of R. exulans have been proposed based on morphological studies on previously distinguished subtypes of the species. Here I use the population genetic data and the results of the ancestral area reconstruction to independently infer an origin for the species. Genetic evidence is incompatible with an origin on the Southeast Asian mainland, while it supports the theory of a Lesser Sunda origin.