Cyclic electron flow (CEF) plays an important role in photoprotection for angiosperms under environmental stresses. However, ferns are more sensitive to drought and their water transport systems are not as efficient as those of angiosperms, it is unclear whether CEF also contributes to photoprotection in these plants. Using Microsorum punctatum and Paraleptochillus decurrens, we studied the electron fluxes through both photosystem I (PSI) and photosystem II (PSII) under water stress and their leaf anatomies. Our goal was to determine if CEF functions in the photoprotection of these ferns and, if so, whether CEF stimulation is related to leaf anatomy. Compared with P. decurrens, M. punctatum had thicker leaves and cuticles and higher water storage capacity, but lower stomatal density and slower rate of water loss. During induced drought, the decrease in leaf water potential (Ψleaf) was more pronounced in P. decurrens than in M. punctatum. For both species, the decline in Ψleaf was associated with a lower effective PSII quantum yield, photochemical quantum yield of PSI and electron transport rate (ETR), whereas increases were found in the quantum yield of regulated energy dissipation, CEF and CEF/ETR(II) ratio. Values for CEF and the CEF/ETR(II) ratio peaked in M. punctatum at a light intensity of 500–600 µmol m−2 s−1 vs only 150–200 µmol m−2 s−1 in P. decurrens. Therefore, our results indicate that the stimulation of CEF in tropical ferns contributes to their photoprotection under water stress, and is related to their respective drought tolerance and leaf anatomy.