The research on museum history has shown how national consciousness has influenced museums worldwide. Even in modern museums, in which citizenship and public access are well emphasized, nationalism affects exhibitions. Historical or art museums might be able to operate close to national consciousness. In contrast, how should a science museum, which is based on scientific rationality and is responsible for disseminating scientific knowledge, deal with national consciousness? In this paper, two of Taiwan’s science museums, the National Museum of Natural Science and the Medical Humanities Museum of National Taiwan University, were studied to understand the relationships between biological knowledge and national consciousness in science museums.