Fungal selectivity (range of potential partners) for algal symbionts has been found to vary inlichen associations. Although a large number of studies have focused on the taxonomy and evolution of fungi in the speciose parmelioid clade (Parmeliaceae, Ascomycota), fungal-algal interactions in this ecologically and evolutionarily diverse group remain largely unexplored. In this study we investigated the algal symbionts of Xanthoparmelia fungi in western North America. We generated sequence data from a total of 58 rock shield lichens (Xanthoparmelia fungi Trebouxia algae) collected across three sites in a subalpine community in southern Utah, USA. We explored the role of substrates, secondary metabolite variation, phenotype-based Xanthoparmelia species, mycobiont genetic population clusters, and site-specific differences in structuring assemblages of algae. Our results indicate that Xanthoparmelia fungi associate with a broad range of Trebouxia lineages in a local, subalpine habitat. Most algae sampled form part of the diverse Trebouxia ‘arboricola/gigantea’ clade, while a small number of algae from outside of this clade were also found to associate with the Xanthoparmelia species investigated here. Our results also revealed multiple Trebouxia lineages within the T. ‘arboricola/gigantea’ clade that have not been previously recognized. Furthermore, accumulation curves suggested that additional algal diversity in rock shield lichen communities in the sampled subalpine habitat may be recovered with increased sampling. Overall, we found no clear association of algal clades with traditional phenotype-based Xanthoparmelia species, mycobiont genetic population clusters, distinct extrolites, or substrates. However, our data revealed significant genetic structuring of Trebouxia communities in separate subalpine meadow areas in a relatively homogeneous subalpine community. Significant site-specific differences in Trebouxia diversity in rock shield lichen communities and low selectivity suggest that photobiont flexibility may play an important role in overall successful colonization of rock shield lichens across a wide array of habitats in western North America.