The primal discipline from which pharmacy has developed can be considered as pharmacognosy. This review defines pharmacognosy while reflecting on the latest development and discourse about its justifiability in the educational system in pharmaceutical faculties and the history of development of new drugs under the influence of pharmacognosy. The article defines the status quo of the pharmacognosy area, or more precisely its parts (biology, chemistry, production, and technology) and discusses their connections. It underlines the legitimacy of application of natural drugs in therapy, which is undeniable, and proves that whether a new drug was prepared either synthetically or isolated from a natural source is not important. The overview follows the basic requirements of pharmacognosy, especially its methodology (usage of faster and more effective phyto-analytical methods, reverse pharmacology, and reverse pharmacognosy, in silico methods). Pharmacognosy is confronted by three major challenges in the 21st century that can push it significantly forward: ethnopharmacological sources evaluation, evaluation of nutraceuticals, and pharmacognosy of marine organisms. The educational system of universities should correspond to these new demands. However, in some areas the educational system is not prepared to face the challenges of the time. The basic requirement is to adopt a complex attitude to biogenic material and utilize the connections of this complexity in the teaching of modern pharmacy.