Lichens that reproduce by means of vegetative propagules (soredia or isidia) are generally thought to have broad geographic distributions. However, recent studies have shown that some asexually reproducing lichens with broad distribution may be comprised of multiple, independent species-level lineages. Our understanding of species diversity in asexually reproducing lichenized fungal species may be further confounded by the fact that otherwise morphologically similar taxa separated based on the presence or absence of vegetative reproductive structures may in fact be conspecific. In this study, we investigate genetic diversity of the pantropical sorediate species Hypotrachyna sorocheila using molecular sequence data. Specifically, we generated a three-marker dataset for Hypotrachyna subgen. Everniastrum specimens, and reconstructed a multilocus, molecular phylogeny. Our results show that sorediate samples phenotypically identifiable as H. sorocheila do not form a monophyletic group, but form two distinct species-level lineages. Although our data support the pantropical distribution of H. sorocheila s.str., including populations in East Africa, a distinct species-level clade was found in Asia and is described as a new species here, H. himalayana Divakar & Kirika sp. nov. This study highlights the fact that the taxonomic significance of reproductive traits may vary among lineages of lichen-forming fungi, and that there is need for careful case-by-case studies.