The rise of sedimentary ancient DNA (sedaDNA) studies has opened up new possibilities for studying pre-historic ecology. The use of sediments to identify organisms even where macroscopic remains are limited or no longer exist is an exciting and potentially ground-breaking area of genomics. There are special considerations however when managing this substrate in Indigenous Australian contexts. Sediments and soils are often considered as waste by-products during archaeological and paleontological excavations, and as such are not typically considered of high value in ethical considerations in traditional western research. Nevertheless, the product of sedaDNA work – genetic information from past fauna, flora, microbial communities, and human ancestors – is likely to be of cultural value for Indigenous peoples. We argue that the integration of Traditional Knowledges into sedaDNA research would a) allow identification of sensitive, secret, or sacred genomic data, and b) improve research outcomes by providing ecological context for species through multi-millennia oral histories.