The defining characteristics of the Lepidodendrales are their secondary xylem, extensive periderm development, three-zoned cortex, rootlike appendages known as stigmarian rootlets arranged in a spiralling pattern, and megasporangium each containing a single functional megaspore that germinates inside the sporangium.

The underground organs of Lepidodendrales typically consisted of dichotomizing axes bearing helically arranged, lateral appendages serving an equivalent function to roots.

[5] The most common fossil specimens of Lepidodendrales, as well as the most recognizable, are the compressions of stem surfaces marked with constant, though partially asymmetric, rhomboidal leaf cushions.

These fossils look much like tire tracks or alligator skin, lending the Greek name "Lepidodendrales," meaning "scale trees."

The central and always present pit results from a vascular bundle that extended into the leaf from the stem, known as "parichnos," a system of aerating tissues.

Unlike modern woody trees, the secondary xylem of Lepidodendrales is only a small portion of the diameter of the stem, as the extensively developed periderm is responsible for the large trunks.

[6] The loose construction of the cortex and the large amounts of thin-walled periderm contributed to the sloughing of tissue layers during the fossilization process.

When plants are immature, the cortex is extensive and the outer stem surface is covered with many rows of leaf bases.

[14] Along the entire lamina of Lepidophylloides, a single vascular bundle is bordered by shallow grooves on the abaxial surface.

[15] The stigmarian organs originate from the base of the trunk as four major axes extending horizontally, leading to a relatively shallow rooting system.

These appendages would abscise as the plant grew, resulting in the characteristic circular external scars of Stigmaria fossil specimens.

Although these appendages are often called "stigmarian rootlets," their helical arrangement and growth abscission are actually more characteristic of leaves than modern lateral roots.

The four primary axes of Stigmaria dichotomize often, forming an extensive underground system possibly ranging up to 15 m (49 ft) in radius.

The secondary xylem tracheids are arranged in radial lines and contain scalariform wall thickenings with fimbrils identical to those in the aerial branches.

These features of the rootlets suggest that they are homologous to the aerial leaves of Lepidodendrales but modified to serve anchoring and absorbing functions.

[23] The embryo begins as an unvascularized globular structure found within megagametophyte tissue, and in more mature specimens two vascularized appendages extend through the trilete suture, representing the first shoot and first root.

Gametophyte generation of Lepidodendrales is poorly understood and based on few specimens, but the Flemingites schopfii cones exhibit well-preserved signs of the micro and megagametophyte phases.

Other well-preserved Lepidodendrid gametophytes have been found in spores of Lepidodendron rhodumnense fossilized in chert from the late Viséan.

[25] During the early stages of growth, arborescent lycophytes grew as unbranched trunks, with the leaves growing directly out of the leaf cushions/bases.

[26] The large quantities of biomass that were responsible for the formation of globally widespread Carboniferous coal seams were predominantly produced by arborescent lycophytes.

[6] Some scientists have suggested that the decline of lepidodendrids during this period was a result of Variscan tectonic activity creating unstable conditions by reducing the size of the coal-swamp ecosystems,[29] while others suggest that their decline was due to climate change; some scientists suggest a combination of these theories, that tectonic activity caused changes in floral composition which triggered climate change, in turn resulting in this decline.

[30] Amongst Lycopodiopsida, Lepidodendrales are considered to be more closely related to Isoetales (which includes modern quillworts) than to club mosses or spikemosses.

[32] Various specimens of Lepidodendrales have been historically categorized as members of Lepidodendron, a genus defined by morphology of leaf cushions.

Synapomorphies of the family Lepidodendraceae are a bilaterally flattened megasporangium and infrafoliar parichnos which extend below the leaf scar.

Specifically, the generic name Lepidodendron is typically used to describe compression specimens which feature a particular type of leaf cushion morphology.