The ability to green in the dark represents a trait providing shade tolerance in seedlings of Norway spruce. In contrast to angiosperm plants, gymnosperms possess two different enzymes for the reduction of protochlorophyllide to chlorophyllide: dark-operative, light-independent protochlorophyllide oxidoreductase (DPOR), consisting of three subunits: ChlL, ChlN and ChlB, and light-dependent protochlorophyllide oxidoreductase (LPOR). European larch seedlings (Larix decidua Mill.), in contrast to Norway spruce (Picea abies Karst.), accumulate only very low amounts of chlorophylls in the dark due to an inactive DPOR enzyme. In this study, we used these two species to investigate the advantage of the co-existence of two protochlorophyllide oxidoreductases on chlorophyll synthesis under different light conditions. We found that under deep shade conditions, the larch seedlings are partially etiolated with a low quantum yield of photosystem II photochemistry caused by inefficient LPOR function under that subliminal irradiance concomitant with an inactive DPOR enzyme. In contrast, spruce accumulated a significant amount of chlorophylls under deep shade conditions due to the co-existence of active DPOR and LPOR enzymes. Moreover, although PSII developed in the dark had an inactive oxygen-evolving complex, even very low irradiance is sufficient for photoactivation of PSII, as proved by the high quantum yield of photosystem II (Fv/Fm) and the disappearance of the K-step in chlorophyll a fluorescence induction under deep shade conditions in spruce. We did not find any advantage of having DPOR enzyme under high light conditions, which is consistent with the decreasing abundance of DPOR subunits with increasing light intensities. Thus, the presence of an active DPOR enzyme may represent a molecular basis for shade tolerance in coniferous seedlings.