Whakapapa is the foundation of traditional Maori social structure and it perpetuates a value base that locates people through their relationships to the physical and spiritual worlds. As part of a new envirogenomics research programme, researchers at the Institute of Environmental Science and Research (ESR) are developing a study with an iwi (tribe) to identify combinations of genetic and environmental factors that may contribute to current health status. A major objective of this study is to utilise whakapapa (genealogical information) to explore patterns of genetic variation unique to the iwi and to correlate these with potential disease or ill health. Genetic testing and screening raises numerous ethical issues, particularly when indigenous peoples are the subjects. This paper will outline ESR's strategy for addressing indigenous concerns about genetic testing and how whakapapa forms an integral part of the envirogenomics research programme.