This study examines two significant research papers on the biological classification system. It aims to clarify methods for comprehending the development of research content in phylogenetic systematics and the comparative view of research papers on the subject. Furthermore, it also attempts to derive the methods’ implications on the research of teaching materials in terms of the kind of expected learning effect when teachers teach phylogenetic systematics units. The study focuses on Whittaker’s (1969) proposal of the 5-kingdom system and on the paper concerning Woese et al.’s (1990) proposal of the 3 domains. It compares and examines their “research methods,” “influences from other areas,” and “background flow.” The results reveal that changes in research resources, such as the development of information gathering technology and developments in other academic areas, have influenced the methodology and classification system of phylogenetic systematics. It also indicates that changes in research methods and developments in other academic areas, whilst being interrelated, have influenced phylogenetic systematics and there exists a critical flow and awareness of the problem that was penetrating the area of research. Moreover, it shows that by comparing the target studies’ effects on subsequent research, the content discussed in each of the papers could be organized much more objectively and the target papers’ points could be much more easily comparable. Furthermore, when investigating how the reading of these papers was reflected in research on teaching materials, the results suggest that by reading and comparing the development of the research content, scientific properties could be taught more efficiently, and it led to a deeper understanding of the phylogenetic systematics unit.