Plant anatomy or phytotomy is the general term for the study of the internal structure of plants. Originally it included plant morphology, the description of the physical form and external structure of plants, but since the mid-20th century plant anatomy has been considered a separate field referring only to internal plant structure. Plant anatomy is now frequently investigated at the cellular level, and often involves the sectioning of tissues and microscopy.
Some studies of plant anatomy use a systems approach, organized on the basis of the plant's activities, such as nutrient transport, flowering, pollination, embryogenesis or seed development.  Others are more classically divided into the following structural categories:
- Flower anatomy, including study of the Calyx, Corolla, Androecium, and Gynoecium
- Leaf anatomy, including study of the Epidermis, stomata and Palisade cells
- Stem anatomy, including Stem structure and vascular tissues, buds and shoot apex
- Fruit/Seed anatomy, including structure of the Ovule, Seed, Pericarp and Accessory fruit
- Wood anatomy, including structure of the Bark, Cork, Xylem, Phloem, Vascular cambium, Heartwood and sapwood and branch collar
- Root anatomy, including structure of the Root, root tip, endodermis
About 300 BC Theophrastus wrote a number of plant treatises, only two of which survive, Enquiry into Plants (Περὶ φυτῶν ἱστορία), and On the Causes of Plants (Περὶ φυτῶν αἰτιῶν). He developed concepts of plant morphology and classification, which did not withstand the scientific scrutiny of the Renaissance.
A Swiss physician and botanist, Gaspard Bauhin, introduced binomial nomenclature into plant taxonomy. He published Pinax theatri botanici in 1596, which was the first to use this convention for naming of species. His criteria for classification included natural relationships, or 'affinities', which in many cases were structural.
It was in the late 1600s that plant anatomy became refined into a modern science. Italian doctor and microscopist, Marcello Malpighi, was one of the two founders of plant anatomy. In 1671 he published his Anatomia Plantarum, the first major advance in plant physiogamy since Aristotle. The other founder was the British doctor Nehemiah Grew. He published An Idea of a Philosophical History of Plants in 1672 and The Anatomy of Plants in 1682. Grew is credited with the recognition of plant cells, although he called them 'vesicles' and 'bladders'. He correctly identified and described the sexual organs of plants (flowers) and their parts.
In the eighteenth century, Carl Linnaeus established taxonomy based on structure, and his early work was with plant anatomy. While the exact structural level which is to be considered to be scientifically valid for comparison and differentiation has changed with the growth of knowledge, the basic principles were established by Linnaeus. He published his master work, Species Plantarum in 1753.
In 1802, French botanist Charles-François Brisseau de Mirbel, published Traité d'anatomie et de physiologie végétale (Treatise on Plant Anatomy and Physiology) establishing the beginnings of the science of plant cytology.
In 1812, Johann Jacob Paul Moldenhawer published Beyträge zur Anatomie der Pflanzen, describing microscopic studies of plant tissues.
In 1813 a Swiss botanist, Augustin Pyrame de Candolle, published Théorie élémentaire de la botanique, in which he argued that plant anatomy, not physiology, ought to be the sole basis for plant classification. Using a scientific basis, he established structural criteria for defining and separating plant genera.
In 1830, Franz Meyen published Phytotomie, the first comprehensive review of plant anatomy.
In 1838 German botanist Matthias Jakob Schleiden, published Contributions to Phytogenesis, stating, "the lower plants all consist of one cell, while the higher plants are composed of (many) individual cells" thus confirming and continuing Mirbel's work.
A German-Polish botanist, Eduard Strasburger, described the mitotic process in plant cells and further demonstrated that new cell nuclei can only arise from the division of other pre-existing nuclei. His Studien über Protoplasma was published in 1876.
Gottlieb Haberlandt, a German botanist, studied plant physiology and classified plant tissue based upon function. On this basis, in 1884 he published Physiologische Pflanzenanatomie (Physiological Plant Anatomy) in which he described twelve types of tissue systems (absorptive, mechanical, photosynthetic, etc.).
British paleobotanists Dunkinfield Henry Scott and William Crawford Williamson described the structures of fossilized plants at the end of the nineteenth century. Scott's Studies in Fossil Botany was published in 1900.
Following Charles Darwin's Origin of Species a Canadian botanist, Edward Charles Jeffrey, who was studying the comparative anatomy and phylogeny of different vascular plant groups, applied the theory to plants using the form and structure of plants to establish a number of evolutionary lines. He published his The Anatomy of Woody Plants in 1917.
The growth of comparative plant anatomy was spearheaded by British botanist Agnes Arber. She published Water Plants: A Study of Aquatic Angiosperms in 1920, Monocotyledons: A Morphological Study in 1925, and The Gramineae: A Study of Cereal, Bamboo and Grass in 1934.
Following World War II, Katherine Esau published, Plant Anatomy (1953), which became the definitive textbook on plant structure in North American universities and elsewhere, it was still in print as of 2006. She followed up with her Anatomy of seed plants in 1960.
- Raven, P. H.; Evert, R. F. and Eichhorn, S. E. (2005) Biology of Plants (7th edition) W. H. Freeman, New York, page 9, ISBN 0-7167-1007-2
- Hagemann, Wolfgang (1992). "The Relationship of Anatomy to Morphology in Plants: A New Theoretical Perspective". International Journal of Plant Sciences. 153 (3(2)): S38–S48. doi:10.1086/297062. JSTOR 2995526.
- Evert, Ray Franklin and Esau, Katherine (2006) Esau's Plant anatomy: meristems, cells, and tissues of the plant body - their structure, function and development Wiley, Hoboken, New Jersey, page xv Archived 2013-12-31 at the Wayback Machine, ISBN 0-471-73843-3
- Howell, Stephen Herbert (1998). Molecular Genetics of Plant Development. Cambridge, England: Cambridge University Press. p. xiii. ISBN 978-0-521-58784-6.
- See e.g. Craig, Richard & Vassilyev, Andrey. "Plant Anatomy". McGraw-Hill. Archived from the original on 24 July 2010.
- Bolam, J. (1973). "The botanical works of Nehemiah Grew, FRS (1641-1712)". Notes and Records of the Royal Society of London. 27 (2): 219–231. doi:10.1098/rsnr.1973.0017. JSTOR 530999.
- Thomas, Hanshaw H. (1960). "Agnes Arber, 1879–1960". Biographical Memoirs of Fellows of the Royal Society. 6: 1–11. doi:10.1098/rsbm.1960.0021. JSTOR 769330.
- Chaffey, N. (2006). "(Book Review) Esau's Plant Anatomy, Meristems, Cells, and Tissues of the Plant Body: their Structure, Function, and Development. 3rd edn". Annals of Botany. 99 (4): 785–786. doi:10.1093/aob/mcm015. PMC 2802946.
- Eames, Arthur Johnson; MacDaniels, Laurence H. (1947). An Introduction to Plant Anatomy 2nd ed. McGraw-Hill, New York, link (1st ed., 1925, link).
- Esau, Katherine (1965). Plant Anatomy 2nd ed. Wiley, New York.
- Meicenheimer, R. History of Plant Anatomy. Miami University, link.
- Cutler, D. F.; Gregory, M.; Rudall, P. (eds.) (1960-2014). Anatomy of the Monocotyledons. 10 vols. Oxford University Press.
- Goffinet, B.; Buck, W. R.; Shaw, J. (2008). Morphology, anatomy, and classification of the Bryophyta. In: Goffinet, B.; Shaw, J. (eds.). Bryophyte Biology, 2nd ed. Cambridge University Press, pp. 55-138 (1st ed., 2000, link).
- Jeffrey, E. C. (1917). The anatomy of woody plants. Chicago, The University of Chicago Press, link.
- Metcalfe, C.R.; Chalk, L. (1957). Anatomy of the Dicotyledons: Leaves, stem and wood in relation to taxonomy, with notes on economic uses. 2 vols. Oxford: Clarendon Press. 1500 pp., link (2nd ed., 1979-1998, 4 vols.).
- Schoute, J. C. (1938). Anatomy. In: Verdoorn, F. (ed.). Manual of Pteridology. Martinus Nijhoff, The Hague. pp. 65—104. link.
- Schweingruber, F. H.; Börner, A.; Schulze, E. (2011-2013). Atlas of Stem Anatomy in Herbs, Shrubs and Trees. Vol. 1, 2011, link. Vol. 2, 2013, link. Springer-Verlag, Berlin, Heidelberg.