Traditional pharmacy and pharmacognosy are two separate academic fields. They are among the PhD courses in the pharmacy discipline in Iran. Traditional pharmacy focuses on studying traditional pharmaceutical texts and producing and evaluating traditional remedies. In contrast, pharmacognosy is the science of extracting, identifying, and studying the therapeutic effects of active compounds found in natural products. The key similarity between these two fields is their use of natural products. However, their distinction lies in their approach to the research methodology on the therapeutic effects of these compounds and their approach toward finished product development. At the academic level, these two fields engage in significant controversies that can shed light on insightful aspects of the relationship between pharmacy and natural products. This study employs a controversy analysis method to identify and analyze 9 peripheral and 3 core controversies. The peripheral controversies cover chemical/herbal, synthetic/natural, formulated/unformulated substance, global standard/local standard, purification/intact compounds, mechanism/evidence, materialistic/spiritualistic, discipline/ field, and professionalism/deprofessionalization. The core controversies, rooted in the philosophical assumptions of each domain, include controversies on intervention in nature/returning to nature, reductionism/holism, and academic knowledge/general-historical knowledge. Analyzing controversies in these academic domains contributes to portraying the position of each discipline from the perspective of the philosophy of science and recognizing their divided missions.