The doctrine of signatures, also known as the doctrine of correspondences, is a biomedicinal theory of pseudoscience. It states that herbs or animals have physical or behavioral traits that mirror the ailment it can successfully treat. Theological justifications, such as that of botanist William Cole, were that God would want to show men what plants would be useful for. The doctrine of signatures has a debated origin. Many historians believe it begins with primitive thinking methods, while other historians believe it originated with Dioscorides and was popularized in the 16th and 17th centuries after Jakob Böhme coined the doctrine of signatures in his book The Signature of All Things.

This theory is a possible explanation for the ancient discovery of medicinal properties; however, there is no definitive proof as to whether the medicinal property or the connection in physical/behavioral traits was realized first. The theory later became a scientific basis for trying new remedies solely based upon their qualities in an attempt to find new medicines. While there are some homeopathic remedies that are still used today which have been connected to this theory, there are also remedies from this theory which have been found harmful. For instance, birthwort (so-called because of its resemblance to the uterus) was once used widely for pregnancies, but is carcinogenic and very damaging to the kidneys, owing to its aristolochic acid content. As a defense against predation, many plants contain toxic chemicals, the action of which is not immediately apparent or easily tied to the plant rather than other factors.

The origins of the doctrine of signatures are debated by historians. The concept of the doctrine of signatures dates back to Hippocratic medicine and the belief that "cures for human ills were divinely revealed in nature, often through plants." The concept would be further developed by Dioscorides. Dioscorides would provide ample descriptions of plant medications through various drawings, detailing the importance of their look, name, shelf life, how to tell when plants have gone bad, and how to properly harvest the crop for medical use. Paracelsus (1493–1541) developed the concept further, writing that "nature marks each growth ... according to its curative benefit", and it was further developed by Giambattista della Porta in his Phytognomonica (1588).

The writings of Jakob Böhme (1575–1624) coined the term "doctrine of signatures" within his book The Signature of All Things (or Signatura Rerum), published in 1621. He suggested that God marked objects with a sign, or "signature", for their purpose, specifically that "to that Signature, his inward form is noted in the form of his face; and thus also is a beast, an herb, and the trees; every thing as it is inwardly [in its innate virtue and quality] so it is outwardly signed". Plants bearing parts that resembled human body parts, animals, or other objects were thought to have useful relevance to those parts, animals, or objects. The "signature" could sometimes also be identified in the environments or specific sites in which plants grew.

The English physician-philosopher Sir Thomas Browne, in his discourse The Garden of Cyrus (1658), uses the quincunx pattern as an archetype of the 'doctrine of signatures' pervading the design of gardens and orchards, botany, and the macrocosm at large.

The 17th-century botanist William Coles supposed that God had made "Herbes for the use of men, and hath given them particular Signatures, whereby a man may read the use of them." Coles's The Art of Simpling and Adam in Eden, stated that walnuts were good for curing head ailments because, in his opinion, "They have the perfect signatures of the head." Regarding Hypericum, he wrote, "The little holes whereof the leaves of Saint Johns wort are full, doe resemble all the pores of the skin and therefore it is profitable for all hurts and wounds that can happen thereunto."

In the late 19th century, Andrew Dickson White published his book History of the Warfare of Science with Theology in Christendom, which pushed back against the doctrine of signatures. White explains the connectiveness between Christianity and the doctrine of signatures as its increased presence and significance in the orthodox faith as theological pseudoscience. White further explains how the doctrine of signatures developed into the church as a justification to "[disgust] the demon with the body which he tormented" and how "the patient was made to swallow or apply to himself various unspeakable ordures", with various uses of animal organs as medications to protect against demons.

For the late medieval viewer, the natural world was vibrant with images of the Deity: 'as above, so below', a Hermetic principle expressed as the relationship between macrocosm and microcosm; the principle is rendered sicut in terra. Michel Foucault expressed the wider usage of the doctrine of signatures, which rendered allegory more real and more cogent than it appears to a modern eye: