The green algal symbionts of the lichenized fungus Letharia are identified as members of the morphospecies Trebouxia jamesii, based on ITS sequences that place them in a molecularly diverse clade with other lichen algae also identified as T. jamesii. However, based on additional sequence from a second locus, actin, T. jamesii is seen to consist of many phylogenetic species. A clade of six to seven closely related phylogenetic species of T. jamesii are symbiotic with five of the six phylogenetic species of Letharia. Within this broad level of specificity, there are also narrower patterns of specificity. For example, three cryptic species of T. jamesii were found only in two species of Letharia in California, a pattern that may be due either to biogeography, or to Letharia phylogenetically tracking Trebouxia. Allopatric Letharia vulpina has switched to a genetically distant phylogenetic species within the T. jamesii morphospecies, suggesting that habitat plays a role in specificity. One phylogenetic species of T. jamesii was found to have a recombining population structure, as two alleles of two loci were found in all four pairwise combinations among the haploid genotypes of that species. This result suggests that Trebouxia, a genus in which sexual structures have never been observed, is nevertheless recombining.