Genetic data, including environmental DNA (eDNA), are regularly used to monitor escalating biodiversity concerns globally. In Aotearoa New Zealand, biodiversity is unique and cherished – many species are taonga (treasured) and cared for by kaitiaki (guardians with customary responsibilities), specifically mana whenua with custodial rights (Māori; the Indigenous people of New Zealand). Discussions are currently underway regarding the development of a reference DNA barcode database for biodiversity in Aotearoa New Zealand to improve outcomes for biosecurity surveillance and taking stock of biodiversity. A priority of these discussions is that the database development and eventual implementation accords with Te Tiriti o Waitangi (The Treaty of Waitangi). Here, we evaluate current practices for storing genetic data from samples collected in Aotearoa New Zealand by examining two major public data repositories – the National Centre for Biotechnology Information (NCBI) GenBank and the Barcode of Life Data System (BOLD). We find that current database practices limit opportunities for Māori sovereignty, with DNA (itself considered taonga) from many taonga species uploaded to public repositories with no associated restrictions or guidelines over use. This is an important finding that will help shape the development of a future reference DNA database for Aotearoa New Zealand that prioritises the rights and interests of Indigenous communities.