Lycophytes represent a diminutive early divergent group of vascular plants recognized as a sister clade of euphyllophytes. As living representatives of lycophytes, many Selaginella species from the rainforest understorey tell us the unique story of an evolution of shade adaptation that occurred in parallel with, and independent of, that of euphyllophytes and especially the angiosperms. Adaptation to deep shade encompasses all levels of a plant’s organization, from habit to the leaf anatomy, from the cell shape to the thylakoid system architecture, the latter dependent on the amount and arrangement of photosynthetic complexes. Given the special evolutionary position of S. martensii, we analysed the thylakoid stacking extent by electron microscopy morphometrics, including grana regularity indexes and differential thylakoid solubilization. We found that S. martensii, instead of a high number of disks per granum, favors a wide granum diameter (>700 nm on average), which constraints the diffusion of long-range electron carriers.