Advances in ancient DNA (aDNA) research have in recent years transformed prehistoric studies and inserted a new level of complexity both in understanding ancient history and in the interactions between archaeologists, geneticists and descent communities. It is especially the case in countries with recognized indigenous peoples, like Taiwan, where most of the prehistoric archaeological research relate to the history of their ancestors or putative ancestors, culturally and genetically. Recent works in the Pacific and the United States have highlighted the potential rewards and pitfalls of aDNA research, not only if it is done through collaborations between archaeologists and geneticists, but also dependent on whether representatives of indigenous communities were involved in the research and analysis. In some cases there has been strong backlash, and a lowering of badly needed trust between archaeologists, scientific institutions, and indigenous stakeholders. In Taiwan, the development of indigenous archaeology is recent and not yet institutionalized, leaving a number of issues linked to ancient DNA research largely untouched or ignored. With these various experiences and background in mind, this presentation attempts to present the current situation in Taiwan in terms of regulations and practice of aDNA analysis on prehistoric remains. It looks at the level of interaction and participation of indigenous communities in the research and analysis and questions how guidelines may be necessary to make the tool of aDNA research beneficial to both the scientific community and indigenous peoples.