The microphylls of Selaginella bear structures that have been given names as diverse as idioblasts, papillae, sclereids, fibers, and warts, yet they resemble silica bodies. However, for most species of the genus, no study has ever shown the composition of these structures or proven their nature comprehensively. Based on scanning electron microscopy and energy dispersive X-ray spectroscopy analyses, we confirmed the presence of silica bodies in microphylls of Selaginella, described four distribution patterns of the structures, and carried out a terminology review. The presence of silica may be related to mechanical protection of the cell wall, activation of defense mechanisms, and providing support for microphylls. Further in-depth analyses based on studies on the evolution of this character remain necessary to elucidate its relevance for the ecological relationships and systematics of Selaginella.