A rapid method to isolate intact functional algae from the lichens Evemia prunastri and Ramalina farinacea has been developed. This method is based on the use of Percoll® gradients after mechanical disruption of lichen thalli. Results obtained show that the algal preparations were virtually free of contamination by fungal hyphae. The purified algal cells were photosynthetically active and without symptoms of photoinhibition, which indicates their functional integrity. This method may be used for the isolation of intact algae from a broad range of lichen species.