This dissertation investigates the cultural and genetic history of the Pukapukan community of Auckland, Aotearoa New Zealand (AoNZ), with a focus on understanding how the distinct history of Polynesia influences health risks for Māori and Pacific individuals. The research integrates ethnographic and genetic approaches, emphasizing the importance of cultural history in shaping scientific research. The ethnography involved interviews with 15 members of the Pukapukan community in Auckland, revealing generational divides between those born in Pukapuka and those born in AoNZ. It also highlighted the community's strong sense of cultural identity, with participants emphasizing their distinct Pukapukan heritage separate from other Cook Island Māori groups. Genetic analysis of 433 individuals with Pukapukan ancestry was conducted to investigate the community's genetic history and its relation to other groups in and outside Polynesia. The study revealed that Pukapukan people are genetically closer to West Polynesian populations than to other Cook Island Māori or New Zealand Māori populations, supporting the community’s belief in their distinct genetic and cultural identity from other Cook Islands populations. The study explored a possible genetic link between Pukapuka and South America, based on oral histories suggesting ancient contact with coastal South American populations, although clear support for this hypothesis was not obtained. The final main chapter explored the role of mitonuclear discordance in the risk of metabolic diseases within Indigenous Māori and Pacific populations in AoNZ. According to the mitonuclear discordance model, differences between mitochondrial DNA and nuclear DNA ancestry can lead to decreased cellular energy efficiency and increased disease risk. Our findings did not support this model, suggesting that factors other than mitonuclear discordance are contributing to the higher rates of metabolic diseases in these communities. Overall, this research underscores the complexity of Polynesian genetic diversity and highlights the need for genetic studies that account for cultural and historical contexts. Through a collaborative and culturally sensitive approach, this work contributes to a more holistic understanding of the relationship between genetic history and health risks in Indigenous Māori and Pacific communities.