Around the world, the repatriation of indigenous remains has long been a contentious issue. Taiwan is no exception. This article examines the Mayuan repatriation case through an institutional lens. It argues that the so-called “repatriation” is much more complex than the physical return of human remains and cultural objects. The process of repatriation is in fact a redefinition of ownership/rights toward the remains/objects, and a reconstruction of relationships between universities, research groups, and more importantly indigenous peoples. It further argues that this case provides us with an opportunity to revisit the fundamental question of who owns/repatriates what, when and how. Given this complexity, this article stresses that providing institutional arrangements is a must. In so doing, the government should show its determination in facing this dark history and then initiate programs, legal proceedings, and fundings to facilitate the return of indigenous ancestral remains/objects to their communities of origin.