Endemic island populations worldwide are at greater risk of extinction than similar mainland populations, in part due to the specific genetic threats faced by small populations, namely of loss of genetic diversity and inbreeding. Reduced genetic diversity limits the ability of populations to adapt to altered conditions, while unavoidable inbreeding reduces population fitness through the effects of inbreeding depression. Effective conservation management requires the understanding of these effects on populations of interest to adopt appropriate strategies to reduce such threats, and thereby ensure long-term population persistence. Through the use of next-generation sequencing, I isolated 11 polymorphic microsatellite loci to allow analysis of current levels of genetic diversity in the endangered Chatham Island black robin Petroica traversi. The black robin has a history of small population size, including a population bottleneck of a single breeding pair, prior to recovery of population size over the past 30 years. The species is currently limited to populations on two small islands, and likely has a high extinction risk due to unavoidable inbreeding in the recovering populations, and may have experienced loss of genetic diversity due to strong genetic drift within these small populations. I compared levels of genetic diversity in the black robin to that of its closest congener, the Chatham Island tomtit Petroica macrocephala chathamensis, to assess how the population history of the black robin has affected its genetic diversity. Additionally, I compared levels of diversity between island populations of each species, to determine whether the smaller populations experienced lower diversity and therefore greater extinction vulnerability. Genetic diversity was lower in the black robin than the tomtit, and lower in the smaller populations of both species. The detection of levels of genetic diversity in the tomtit similar to those of threatened species suggests population viability of this species of least concern may be lower than expected. The two island populations of black robin are thought to have been isolated from one another for 26 years, and so populations were genotyped to determine whether this isolation has resulted in population differentiation, despite the short period of isolation. The two populations show substantial genetic differentiation, indicating genetic drift has had strong independent effects on these isolated populations. Although the tomtit exists on three islands, there was no evidence of current dispersal between the two populations assessed, and there was a similar level of differentiation between these populations and the black robin populations. Over 30 years of observational data show the black robin to be socially monogamous, with no evidence of extra-pair breeding. However, assessment of the social pedigree using microsatellite genotyping found a conservative rate of extra-pair paternity of approximately 14%, and the existence of a low-level of intraspecific brood paternity could not be rejected. As yet, the reason for the evolution of a strategy of extra-pair paternity is unknown. From the results of this study, I recommend reciprocal translocations of black robins between island populations as a form of assisted gene flow to bolster genetic diversity of each population, and to reduce inbreeding in the smaller of the two populations. Furthermore, the establishment of a third population is recommended to minimise extinction vulnerability of this endangered species. As the black robin is not genetically monogamous, selection of individuals for translocation will require the use of molecular techniques to assess relatedness, rather than the social pedigree, to maximise success.