When discussing the religious beliefs of Taiwanese indigenous peoples, scholars in Taiwan often draw parallels between their spirit cults and Han Chinese ancestor worship. On the surface, these two kinds of worship both deal with memorializing and venerating the deceased. However, behind these two systems of religious ceremony are ideas involving the nature of humanity and the relationship between humanity and nature (or the supernatural) that are extremely different. It is only when we carefully examine such practices that we can then elucidate their fundamental differences. On the whole, discussions regarding ancestors and ancestral spirits must be placed within a comparative framework that considers the relationship between both clan and family and spirit and spiritual power. At the same time, scholars should investigate the different religious thinking that each system involves; only then, can we see the different styles and features that emerge from the two systems of religious belief. This paper is a preliminary investigation focusing on the complex facets of this issue.