For decades, lichenologists have developed numerous and varied methods to isolate lichen photobionts. Most procedures are tedious, slow, and require several months after the initial isolation to obtain clones. Furthermore, the purity of the isolated photobionts obtained by more rapid methods is not sufficient to establish phycobiont axenic cultures. We have developed a new method for isolating lichen photobionts from fruticose, foliose and crustose lichens. Basically, it involves homogenization of lichen thalli (from 15 mg to 2 g), a one-step centrifugation through Percoll ®, followed by washing with Tween 20 and sonication. With this simple and rapid method (which takes less than 2 h), photobiont cells are obtained in sufficient quantity and purity to obtain dozens of axenic algal cultures. Keywords Axenic strains . Isolation . Lichen photobionts . Trebouxia.