The endemic Hawaiian Petrel (Pterodroma sandwichensis) is a long-lived pelagic seabird. Although endangered, subfossil evidence indicates that it was formerly more abundant in the past. In addition to a wider distribution on islands where the petrel currently breeds, two colonies, one on Oahu and one on Molokai, have been extirpated since humans colonized the Islands. Despite this, little is known about this species. Here I use conservation genetic and ancient DNA techniques to investigate the taxonomic status and population dynamics of the Hawaiian petrel. Investigation of the timing and magnitude of divergence between the Hawaiian petrel and its sister species, the Galapagos petrel (P. phaeopygia), revealed that these taxa diverged approximately 550,000 years ago. In a phylogenetic tree constructed from mitochondrial data Galapagos and Hawaiian petrels were reciprocally monophyletic, however, trees from the nuclear data set were unresolved. Low estimates of gene flow between taxa indicate that incomplete lineage sorting is causing the difference in resolution between data sets and that Galapagos and Hawaiian petrels are likely separate species. In addition to the mitochondrial and nuclear intron data sets, I developed a suite of 20 polymorphic microsatellite loci: I developed 10 specifically for the Hawaiian petrel, and characterized an 10 additional previously reported loci in this species. Using these three data sets I investigated the pattern of gene flow and divergence between modern, historical, and ancient populations of the Hawaiian petrel. The mitochondrial data set showed strong levels of differentiation between modern populations. The two nuclear data sets also revealed significant population structure, although it was weaker. Mitochondrial DNA sequences obtained from subfossil bones indicate that populations were significantly differentiated in the past, although there was low divergence between the extirpated Oahu and Molokai populations and modern birds from Lanai, suggesting that perhaps as colonies dwindled individuals dispersed to that island. Investigation of the effective population size indicates that no significant change has occurred on Hawaii or Maui. It appears that the long generation time of this species may have allowed it to escape a genetic bottleneck after the arrival of humans in the Hawaiian Islands.