Population genetic methods can be employed to inform the conservation of a species in a number of ways. For instance, they can be used to determine if a species has gone through a genetic bottleneck (i.e. a drastic reduction in population size that results in reduced genetic variation), and also if a species exhibits local genetic structure, (i.e., whether there is population genetic structure among neighbouring populations of an otherwise widely distributed species). The objectives of this thesis were to investigate the population genetic structure and long-term effective population size of the recently rediscovered subspecies of the masked booby, the Tasman booby, Sula dactylatra tasmani, which unlike masked boobies ,which have a pantropical distribution and are widespread, are range restricted to three island groups in the North Tasman Sea. To achieve this, I apply population genetic methods to mitochondrial control region sequence data, and microsatellite genotype, along with morphometric data. I first examined the cross utility of 43 microsatellite loci developed for the blue-footed (S. nebouxii), red-footed (S. sula) and Peruvian (S. variegata) booby for a population genetic study in my focal subspecies, the Tasman booby. All of these loci amplified in the Tasman booby, and from these 13 independent polymorphic loci were found and used as nuclear data, along with mitochondrial sequence data, to estimate population genetic structure. I also used these two types of data to determine the effective population size of this subspecies, both recently and historically. I found strong population genetic structure from the mitochondrial sequence data, while the microsatellite genotype data revealed weak but significant population genetic structure. I suggest the differences in these two types of marker are most likely due to stochasticity in the mitochondrial genome and/or male-mediated gene flow. Combined, the mitochondrial and microsatellite data revealed the Tasman booby has existed at a relatively stable population size for the last 25,000 years, but estimates of the current effective population size of this subspecies were unreliable. From these combined data I recommend that the Tasman booby should be treated as a single management unit, and conservation efforts from Australia and New Zealand could benefit from communication regarding their management plans. Future work including both autosomal and sex-linked introns could help in resolving the presence or absence of male-mediated gene flow, and/or help estimate an accurate effective population size in this subspecies.