In most lichens, the symbiosis between one fungus (mycobiont) and one photosynthetic partner (photobiont) results in a uniform thallus whose morphology is distinctive for each combination of symbionts. In some lichens, two morphologically different thalli, one containing a green alga, the other a cyanobacterium, are joined together in a chimera called photosymbiodeme. The question whether the same or two different mycobionts are involved in the formation of the different chimera components (morphotypes) is relevant to lichen morphogenesis, physiology, and taxonomy, but has not been answered conclusively to date. We have developed nucleic acid extraction procedures suitable for lichens. Using Southern hybridization and the polymerase chain reaction we demonstrate the genetic near-identity of the mycobionts forming paired morphotypes in two different photosymbiodemes. © 1991 Academic Press, Inc.