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Abstract Lichens are major components of high altitude/latitude ecosystems. However, accurately characterizing their biodiversity is challenging because these regions and habitats are often underexplored, there are numerous poorly known taxonomic groups, and morphological variation in extreme environments can yield conflicting interpretations. Using an iterative taxonomic approach based on over 800 specimens and incorporating both traditional morphology‐based identifications and information from the standard fungal DNA barcoding marker, we compiled a voucher‐based inventory of biodiversity of lichen‐forming fungi in a geographically limited and vulnerable alpine community in an isolated sky island in the Colorado Plateau, USA—the La Sal Mountains. We used the newly proposed Assemble Species by Automatic Partitioning (ASAP) approach to empirically delimit candidate species‐level lineages from family‐level multiple sequence alignments. Specimens comprising DNA‐based candidate species were evaluated using traditional taxonomically diagnostic phenotypic characters to identify specimens to integrative species hypotheses and link these, where possible, to currently described species. Despite the limited alpine habitat (ca. 3,250 ha), we document the most diverse alpine lichen community known to date from the southern Rocky Mountains, with up to 240 candidate species/species‐level lineages of lichen‐forming fungi. 139 species were inferred using integrative taxonomy, plus an additional 52 candidate species within 29 different putative species complexes. Over 68% of sequences could not be assigned to species‐level rank with statistical confidence, corroborating the limited utility of current sequence repositories for species‐level DNA barcoding of lichen‐forming fungi. By integrating vouchered specimens, DNA sequence data, and photographic documentation, we provide an important baseline of lichen‐forming fungal diversity for the limited alpine habitat in the Colorado Plateau. These data provide an important resource for subsequent research in the ecology and evolution of lichens alpine habitats, including DNA barcodes for most putative species/species‐level lineages occurring in the La Sal Mountains, and vouchered collections representing any potentially undescribed species that can be used for future taxonomic studies.