The tissues present in young roots, starting with the most external tissue, include an epidermis with root hairs, cortex, endodermis, pericycle, phloem, xylem, and, in some species, pith. In some species, the outermost layer or layers of cortex are distinct from the inner layers, in which case they are referred to as a hypodermis. In species that undergo secondary growth in the roots, it is typical for all tissues external to the pericycle to be sloughed off. Roots that exhibit secondary growth have a periderm or bark, composed of a phellum (cork), phellogen (cork cambium), and phelloderm as the outermost tissue. Underneath the periderm, remnants of primary phloem, secondary phloem, vascular cambium, primary xylem, and secondary xylem can be found. Secondary vascular tissues have medullary rays separating clusters of the principal conducting cells of phloem (sieve elements or sieve cells) and the principal conducting cells of xylem (vessels and tracheids). Most species of plants that undergo secondary growth lack pith in the root. The type and arrangement of the principal conducting cells of the vascular tissues may be diagnostic of the species. Roots of many species develop into food storage organs. Abundant parenchyma and large amounts of starch or other polysaccharides characterize these types of roots. The presence, type, and arrangement of fibers, sclereids, and other tissues, and the presence and location of ergastic material, may also be diagnostic features. Morphologically, roots may be distinguished from rhizomes (the underground stems) primarily by the absence of nodes and internodes, which are present in rhizomes.

Several external macroscopic features of stems that may be diagnostic of the species include the attributes of the nodes, internodes, leaf scars, vascular bundle scars, lenticles, and buds; the growth pattern of the buds; position and arrangement of the leaves along the stem; and the presence of tendrils, spines, thorns, or prickles. Starting with the outermost tissue, the internal arrangement of tissues in the young stems of most species is epidermis, cortex, a concentric ring of vascular bundles separated from each other by parenchymatous medullary rays, and pith. Depending on the species, stomata or trichomes or both structures may be present in the epidermis. The cortex of some species may include a hypodermis or an endodermis or both. In most monocotyledons, the vascular bundles are not arranged concentrically; instead, they are scattered throughout a mass of parenchyma tissue internal to the epidermis. Because of this arrangement, neither cortex, medullary rays, nor pith can be discerned. In woody plant stems that undergo secondary growth, it is typical for the epidermis to be sloughed off and replaced by a periderm composed of a phellum, phellogen, and phelloderm. Some species are characterized by having multiple periderms (rhytidome). Lenticles may be present in the periderm and their attributes may serve as diagnostic features. Underneath the periderm are the remnants of the cortex, primary phloem, secondary phloem, vascular cambium, secondary xylem, primary xylem, and pith. Medullary rays are also present. As in the root, the type and arrangement of the principal conducting cells of the vascular tissues; the presence, type, and arrangement of fibers, sclereids, and other tissues; and the presence and location of ergastic material may also be diagnostic features. Rhizomes may have some morphological characteristics similar to those of roots and therefore they may be mistaken for roots. However, rhizomes can be correctly identified as stems because they have distinct nodes and internodes.

Several macroscopic features of leaves that may be diagnostic of the species include the attributes of the leaf blade, petiole, and stipules and the phyllotaxy. The outermost tissue of a leaf blade is the epidermis, followed by mesophyll and vascular tissues. Microscopic diagnostic features of epidermal cells include the cuticle thickness and markings, the shape and arrangement of stomata and guard cells, the arrangement and size of subsidiary cells, stomatal number (number of stomata per unit area), and stomatal index (number of stomata per unit number of epidermal cells). Additional features useful in the identification of leaf material include types and arrangement of trichomes (plant hairs) present; type and arrangement of mesophyll and vascular tissues; palisade mesophyll ratio; presence and appearance of accessory tissues such as parenchymatous or sclerenchymatous bundle sheaths, paraveinal mesophyll, endodermis, and transfusion tissue; type and arrangement of the principal conducting cells of the vascular tissues; presence, type, and arrangement of fibers, sclereids, and other tissues; and presence, location, and physical appearance of ergastic material.

Flowers are the best diagnostic morphological features of any flowering plant, and the floral structure is the principal criterion used in plant taxonomy. The diagnostic features of flowers include type of inflorescence; presence, number, and appearance of the primary floral parts (sepals, petals, stamens, and carpels); type of symmetry displayed by the floral parts; relative position of the ovaries in regard to the other parts of the flower; the number of ovules per ovary; type of placentation of the ovary; physical appearance of the pollen grains; presence of nectaries; presence of covering or glandular trichomes; and physical features of accessory structures such as the receptacle and bracts. The histological features and the presence of ergastic materials in the tissues of floral parts are also diagnostic of the species.

The identification of the species of plant from which a fruit was derived may be determined by observing several macroscopic criteria. These criteria include the number of pistils found in the fruit; the number of carpels within each pistil; the number of seeds within each carpel; the placentation of the fruit; and the determination of whether the fruit is dehiscent, indehiscent, or fleshy. Additional diagnostic features include the number of sutures in a dehiscent fruit, the determination of whether the seeds are fused to or free from the pericarp wall, physical features of the three layers of the pericarp of fleshy fruits (epicarp, mesocarp, and endocarp), and presence and physical appearance of accessory tissues such as the receptacle and bracts. Histological features of fruit tissues may aid in identification. The characteristics of the seeds within the fruit are also diagnostic features of the species.

The macroscopic features of seeds used in identification include the shape and size of the seed; appearance of the seed-coat surface; placement of the hilum and micropyle; and presence of accessory structures of the seed coat such as the arils, caruncle, or oil bodies. Physical features of the embryo, such as its size, shape, position, and the number and appearance of the cotyledons, as well as the presence and appearance of accessory nutritive tissues such as the remnants of a megagametophyte (in gymnosperms), perisperm (nucellus), or endosperm, are also diagnostic of the species. Histological features of the seed coat and other structures and tissues of the seed may also be used for species identification.

When it is necessary to reveal detailed histological features of a plant specimen, thin tissue sections have to be obtained. The sections need to be thin enough to transmit light, and they have to be cut in such a plane that the desired features are exposed. The plant material is properly killed, fixed, dehydrated, and embedded in paraffin or other embedding media. The embedding medium is used as a solid-support matrix during tissue sectioning. After sectioning and mounting, staining of the specimen is frequently performed to aid in the differentiation of certain structures. [Note—The process of fixing, dehydration, embedding, and staining can be significantly expedited by utilizing a microwave oven specifically designed for histological work. ]

The chosen sequence must be sufficiently specific to capture any potential primary and adulterant species in the sample but also sufficiently universal to avoid false-negative reactions for closely related species. For example, a species-specific primer is not appropriate for most identification procedures because adulterants cannot be detected and amplification failure can result because of either the absence of the species or degraded DNA. In many cases, a single marker may be sufficient for identification, but multiple markers from different parts of the genome (e.g., plastid or nuclear material) ensure that hybrids can be detected. Typically, regions used for DNA sequence identification range from 100–1500 base pairs in length. Smaller DNA fragments may be less susceptible to DNA degradation.

Before amplification of the desired marker can be performed, the total genomic DNA must be extracted. The suitability of a procedure for genomic extraction depends on the starting material and the purity of the DNA required for downstream applications. The principal procedures are described as follows, and several commercial kits are available to accommodate different sample types and applications.

Total genomic DNA must be extracted from ground plant material. Plant materials can be homogenized manually using a mortar and pestle, mechanical grinder, or other apparatus depending on the nature of the material. Total genomic DNA extraction and purification can be challenging because of the abundance of secondary metabolites (polysaccharides, tannins, essential oils, phenolics, alkaloids, and waxes) in many medicinal plant species. Some of the secondary metabolites may coprecipitate with DNA during extraction and may inhibit further enzymatic reactions, including restriction digestion and PCR. In particular, large amounts of complex polysaccharides can make extraction of usable DNA impossible, rendering the aqueous portion of the extract too viscous to allow efficient separation of DNA from the contaminating polysaccharides. This type of contamination can lead to poor DNA yield and can prevent access by modifying enzymes.

Numerous commonly used DNA extraction methods are appropriate for a wide range of fresh and dried plant materials, including cetyl trimethylammonium bromide, silica-based methods, and a variety of commercially available kits that use silica columns or glass-coated magnetic beads. Although many of these methods work well on both fresh and dried materials and on any plant part, those that are degraded or contain significant levels of secondary compounds or other PCR inhibitors may require minor adjustments to standard extraction protocols.

Typically, PCR primers are between 18 and 30 bases in length and amplify a region between 100 and 1500 base pairs in length. As noted, PCR primers may be universal, meaning they are capable of amplifying all potential organisms that are present in a test sample (including fungi, plants, and animals or an important and predicable subset), or they are taxon specific, meaning they have been designed to amplify only organisms in a targeted set (i.e., family, genus, species, or subspecies). A number of nuclear, mitochondrial, and plastid gene regions are used for universal amplification, including nrITS, nrITS1, nrITS2, matK, rbcL, psbA–trnH intergenic spacer, cox3, COI (also known as cox1), external transcribed spacer, 18S, 5S, trnL–trnF intergenic spacer, and trnL intron. Taxon-specific primers may be designed on the basis of proteins found in specific plant groups (e.g., the soy lectin gene found in soy) or by obtaining sequences of any variable DNA region for the target taxon and designing primers that specifically bind only to sequences from the taxon of interest.