In growth habit, the aerial portions of sporophytes of Lycopodium species may rise erectly from a system of rhizomes (underground stems), or they may creep. Many are epiphytes; i.e., they grow attached to tree branches or other supports. Branching is usually dichotomous, but in species with well-developed rhizomes one branch of a dichotomy usually becomes much longer and larger than the other and remains close to the surface. The shorter one may undergo several limited dichotomies, the ultimate upright branches terminating in strobili. The leaves may be spirally arranged or grouped in four vertical rows along the shoot. Each leaf has one unbranched midvein. Adventitious roots, initiated near the shoot tip, may grow within the stem cortex for some distance before emerging. The roots branch dichotomously, but no extensive root system is formed.

The stem is protostelic (without a central pith), but there is great variety in the disposition of xylem and phloem in the central vascular cylinder. Sporophylls may be aggregated into definite strobili, or there simply may be fertile and sterile regions along a stem, the sporophylls resembling vegetative leaves. Often the sporophylls of compact strobili differ from the vegetative leaves of the same plant.

Selaginella species have foliage leaves only a few millimetres long; they may be dark green or bluish and in some species are iridescent. As in Lycopodium, branching is usually dichotomous. The sporophyte may consist of several upright branches from a rhizome, prostrate branches creeping along the surface of the soil, or large, flat, erect, frondlike side branches from strong rhizome systems. The entire branch system often resembles a fern leaf. One distinctive feature of Selaginella is the rhizophore, a proplike structure that originates at a point of branching and that forks dichotomously after making contact with the soil or a hard surface. Rhizophores are most readily seen in clambering species. Morphologically, the rhizophore is considered to be a root, although on occasion it can give rise to leafy branches if the normally leafy branches are cut off. Anisophylly (the occurrence of two sizes of leaves) occurs in most species of Selaginella, especially those of the wet tropics.

Another distinctive feature in Selaginella is the presence of an unusual structure on the adaxial side of a leaf; this is the ligule, a peculiar tonguelike outgrowth from the leaf surface near the leaf base. Leaves of Lycopodium and Selaginella can be differentiated on this basis. The ligule, which appears very early in the development of a leaf, is a surprisingly complex structure at maturity. Its evolutionary origin is obscure. Functionally, ligules are believed to be secretory organs that, by exuding water and possibly mucilage, serve to keep young leaves and sporangia moist. Short-lived structures, they become shrunken and inconspicuous in older leaves. The ligule was a characteristic feature of the extinct giant lycophytes such as Lepidodendron.

Isoetes species have a plant body that is relatively small, consisting of a short compact axis (corm) and tufts of leaves and roots. Many species are similar in appearance to certain aquatic grasses and other aquatic flowering plants. The majority of species occur in the cooler regions of the world and are often immersed continuously in water. Each leaf is actually a sporophyll, bearing either a microsporangium or a megasporangium which is embedded in its base on the adaxial side. Each leaf also has a ligule, similar to that of Selaginella. Isoetes differs from both Selaginella and Lycopodium in the occurrence of secondary growth in the stem and the possession of a definite root-producing meristem. The sets of roots arise in a definite sequence, in contrast to the more or less irregularly produced roots of all other extant lower vascular plants. This sequence resembles that of its presumed ancestors Lepidodendron and Pleuromeia.

Cytogenetics

As in the ferns, the heterosporous representatives have much lower chromosome numbers than do the homosporous groups. Thus, Selaginella and Isoetes have x = 9 or 10 (Selaginella) and 11 (Isoetes), whereas Lycopodium and Phylloglossum have a wide range of higher numbers, which are correlated with subgenera or genera: x = 23 (Diphasiastrum), 34 (Lycopodium in the strict sense), 35 (Pseudolycopodiella), 39 (Lycopodiella), 67 to 68 (Huperzia and Phlegmariurus), and 104 to 156 (Palhinhaea). Phylloglossum has x = about 250. Hybridization is rare in Selaginella but common in Isoetes and the terrestrial species of Lycopodium.