Willeya is a recently resurrected genus comprising crustose pyrenolichens common on rock in terrestrial habitats in southeastern Asia, Australasia, and eastern North America. The generic type W. diffractella is endemic to eastern North America, and is currently delimited to include considerable morphological and ecological variation. Previous molecular studies including W. diffractella have included sequences from a single specimen, which is morphologically distinct and ecologically discordant from the lectotype. Here we examine the delineation of W. diffractella using ITS sequences from 21 specimens and two specimens of Endocarpon tenuissimum, a closely related Appalachian endemic. Our results show that: 1) E. tenuissimum is nested within a monophyletic W. diffractella, and thus E. tenuissimum is placed in synonymy, 2) morphological variation within W. diffractella does not correlate with phylogeny, affirming that the observed variability is infraspecific, 3) there is no phylogenetic structure corresponding to biogeographic patterns within W. diffractella, and 4) within W. diffractella all but one sample from calcareous substrates clustered within a single well-supported lineage, suggesting an avenue for further study.