Chlorophyll a fluorescence was used to look at the effect of desiccation on the photophysiology in two beachrock microbial biofilms from the intertidal rock platform of Heron Island, Australia. The photophysiological response to desiccation differed between the beachrock microbial communities. The black biofilm from the upper shoreline, dominated by Calothrix sp., showed a response typical of desiccation-tolerant cyanobacteria, where photosynthesis closed down during air exposure with a rapid and complete recovery upon rehydration. In contrast, the pink biofilm from the mid-intertidal zone, dominated by Blennothrix sp., showed no distinct response to desiccation stress and instead maintained reduced photosynthesis throughout drying and re-wetting cycles. Spatial differences in photosynthetic activity within the black biofilm were evident with a faster recovery rate of photosynthesis in the surface cyanobacteria than in the deeper layers of the biofilm. There was no variation with depth in the pink biofilm. The photophysiological differences in desiccation responses between the beachrock biofilms exemplify the ecological niche specialisation of these complex microbial communities, where the functional differences help to explain their vertical distribution on the intertidal shoreline.