Photosynthetic electron transport of beachrock microbial mats growing in the intertidal zone of Heron Island (Great Barrier Reef, Australia) was investigated with a pulse amplitude modulation chl fluorometer providing four different excitation wavelengths for preferential excitation of the major algal groups (cyanobacteria, green algae, diatoms/dinoflagellates). A new type of fiberoptic emitter‐detector unit (PHYTO‐EDF) was used to measure chl fluorescence at the sample surface. Fluorescence signals mainly originated from cyanobacteria, which could be almost selectively assessed by 640‐nm excitation. Even after desiccation for long time periods under full sunlight, beachrock showed rapid recovery of photosynthesis after rehydration in the light (t1/2∼ 15 min). However, when rehydrated in the dark, the quantum yield of energy conversion of PSII remained zero over extended periods of time. Parallel measurements of O2concentration with an oxygen microoptode revealed zero oxygen concentration in the surface layer of rehydrated beachrock in the dark. Upon illumination, O2concentration increased in parallel with PSII quantum yield and decreased again to zero in the dark. It is proposed that oxygen is required for preventing complete dark reduction of the PSII acceptor pools via the NADPH‐dehydrogenase/chlororespiration pathway. This hypothesis is supported by the observation that PSII quantum yield could be partially induced in the dark by flushing with molecular oxygen.Abbreviations:EDF, emitter‐detector unit; Fo, fluor‐escence yield of dark‐adapted sample; Fm, maximal fluorescence yield measured during saturation pulse; Fv, variable fluorescence yield; LED, light‐emitting diode; PAM, pulse amplitude modulation; PQ, plastoquinone