Indigenous peoples around the world are leading discusions regarding genomic research of humans, and more recently, species of cultural significance, to ensure the ethical and equitable use of DNA. Within a Maori (indigenous people of Aotearoa New Zealand) worldview, genomic data obtained from taonga (treasured) species has whakapapa - generally defined as genealogy, whakapapa layers the contemporary, historical and mythological aspects of bioheritage - thus genomic data obtained from taonga species are taonga in their own right and are best studied using Maori principles. We contend it is the responsibility of researchers working with genomic data from taonga species to move beyond one-off Maori consultation toward building meaningful relationships with relevant Maori communities. Here, we reflect on our experience embedding Maori principles in genomics research as leaders of a BioHeritage National Science Challenge project entitled 'Characterising adaptive variation in Aotearoa New Zealand's terrestrial and freshwater biota'. We are co-developing a culturally-responsive evidence-based position statement regarding the benefits and risks of prioritising adaptive potential to build resilience in threatened taonga species, including species destined for customary or commercial harvest. To achieve this, we co-developed a research programme with the local subtribe, Ngai Tuahuriri, that integrates Maori knowledge with emerging genomic technologies and extensive ecological data for two taonga species, kowaro (Canterbury mudfish; Neochanna burrowsius) and kekewai (freshwater crayfish; Paranephrops zealandicus). The foundation of our research programme is an iterative decision-making framework that includes tissue sampling as well as data generation, storage and access. Beyond upholding the promises made in The Treaty of Waitangi, we contend the integration of Maori principles in genomics research will enhance the recovery of taonga species and enable the realisation of Maori values.