Shifts in climate along elevation gradients structure mycobiont-photobiont associations in lichens. We obtained mycobiont (lecanoroid Lecanoraceae) and photobiont ( alga) DNA sequences from 89 lichen thalli collected in Bolivia from a ca. 4,700 m elevation gradient encompassing diverse natural communities and environmental conditions. The molecular dataset included six mycobiont loci (ITS, nrLSU, mtSSU, , , and ) and two photobiont loci (ITS, L); we designed new primers to amplify Lecanoraceae and with a nested PCR approach. Mycobionts belonged to s.lat., , , , the " " group, and the " ." saligna group. All of these clades except for s.lat. occurred only at high elevation. No single species of Lecanoraceae was present along the entire elevation gradient, and individual clades were restricted to a subset of the gradient. Most Lecanoraceae samples represent species which have not previously been sequenced. clade C, which has not previously been recorded in association with species of Lecanoraceae, predominates at low- to mid-elevation sites. Photobionts from clade I occur at the upper extent of mid-elevation forest and at some open, high-elevation sites, while clades A and S dominate open habitats at high elevation. We did not find clade D. Several putative new species were found in clades A, C, and I. These included one putative species in clade A associated with species growing on limestone at high elevation and a novel lineage sister to the rest of clade C associated with on bark in low-elevation grassland. Three different kinds of photobiont switching were observed, with certain mycobiont species associating with from different major clades, species within a major clade, or haplotypes within a species. Lecanoraceae mycobionts and photobionts exhibit species turnover along the elevation gradient, but with each partner having a different elevation threshold at which the community shifts completely. A phylogenetically defined sampling of a single diverse family of lichen-forming fungi may be sufficient to document regional patterns of diversity and distribution.