The Lycophyte Selaginella martensii efficiently acclimates to diverse light environments, from deep shade to full sunlight. The plant does not modulate the abundance of the Light Harvesting Complex II, mostly found as a free trimer, and does not alter the maximum capacity of thermal dissipation (NPQ). Nevertheless, the photoprotection is expected to be modulatable upon long‐term light acclimation to preserve the photosystems (PSII, PSI). The effects of long‐term light acclimation on PSII photoprotection were investigated using the chlorophyll fluorometric method known as “photochemical quenching measured in the dark” (qPd). Singularly high‐qPd values at relatively low irradiance suggest a heterogeneous antenna system (PSII antenna uncoupling). The extent of antenna uncoupling largely depends on the light regime, reaching the highest value in sun‐acclimated plants. In parallel, the photoprotective NPQ (pNPQ) increased from deep‐shade to high‐light grown plants. It is proposed that the differences in the long‐term modulation in the photoprotective capacity are proportional to the amount of uncoupled LHCII. In deep‐shade plants, the inconsistency between invariable maximum NPQ and lower pNPQ is attributed to the thermal dissipation occurring in the PSII core.