Lichens, a classic example of an obligate symbiosis between fungi and photobionts (which could be algae or cyanobacteria), are abundant in many terrestrial ecosystems. The genetic structure of the photobiont population found in association with a lichen-forming fungal species could be affected by fungal reproductive mode and by the spatial extent of gene flow in the photobiont. Using DNA sequences from one nuclear ribosomal and two chloroplast loci, we analyzed the genetic structure of the photobiont associated with the fungus Ramalina menziesii at an oak woodland study site in southern California. We had previously shown that the fungus exhibited no genetic structure among four local sites or three phorophyte species. Our goals were to identify the photobiont species and assess its genetic structure. We found that R. menziesii was highly specific in its photobiont choice and associated with one alga, Trebouxia decolorans. In contrast to the fungal population, we found significant differentiation among the algae sampled on three oak species and little genetic structure among the sites for two of the three algal loci. We hypothesize that R. menziesii is locally adapted to the phorophyte species through habitat specialization in the algal partner of the symbiosis.