Premise of research. We examined select members of the Lycopodiaceae (Lycopodioideae and Huperzioideae) and Selaginellaceae to determine whether there were some unique anatomical and histochemical traits that might contribute to our understanding of their stems and roots.Methodology. Living plants and herbarium/dried specimens were examined using hand or hand microtome sections, processed in different stains, and viewed using different microscopic methods.Pivotal results. Among the Lycopodiaceae, Lycopodioideae, the innermost region of the cortex in stems and roots often has variously modified cell walls that we term an endodermoid without Casparian bands. In the Huperzioideae, the cell walls of the innermost cortex usually have a layer of cells better defined as an endodermis because cells with Casparian bands are usually evident in a ring around the stele of stems and vascular cylinder of roots. Lycopodioideae adventitious roots have an epidermal emergence from the stems, while Huperzioideae roots have a cortical emergence. Stems of Selaginellaceae do not have a well-defined endodermis or endodermoid around their steles; instead, most species studied have an extracellular wall layer lining outer stele and inner cortical trabecular cells, interpreted as a stele-cortex wall that is readily apparent only under 488-nm laser microscopy. While most Selaginella species have an endodermis in their rhizophores, roots of all species studied have an endodermis with Casparian bands and often with suberin lamellae.Conclusions. Our results revealed the occurrence of distinct innermost cortex layers not adequately and previously demonstrated in these plants. In Lycopodiaceae, these are endodermoid or endodermis. In Selaginellaceae, these are extracellular stele-cortex walls in most stems and endodermis in rhizophores and roots. There is clearly a need to examine in much greater detail cell wall chemistry and cell/tissue development as they relate to the genetics and molecular development of these extant lycopods and their phylogenetic history.