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The growth of botany following European expansion and the consequent increase of plants necessitated significant development in classification methodology, during the key decades spanning the late 17th to the mid-18th century, leading to the emergence of a "natural method." Much of this development was driven by the need to accurately identify medicinal plants, and was founded on the principle of analogy, used particularly in relation to properties. Analogical reasoning established correlations (affinities) between plants, moreover between their external and internal characteristics (here, medicinal properties). The diversity of plants, names, and botanical information gathered worldwide amplified confusion. This triggered the systematisation of the collection and referencing of data, prioritizing the meticulous observation of plant characteristics and the recording of medicinal properties as established by tradition: it resulted in principled methods of natural classification and nomenclature, represented by the genus, to enhance reliability of plant knowledge, which was crucial in medical contexts. The scope of botany increased dramatically, with new methods broadening studies beyond traditional medicinal plants. The failure of chemical methods to predict properties, particularly of unknown flora, amplified the reliance on analogy and on natural affinities., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)