The Lepraria neglecta group is a distinctive entity within the sterile, asexually reproducing lichen genus Lepraria whose constituent populations are united by their occurrence in exposed habitats and the development of a pseudocortex on the granules of the thallus. Previous studies have concluded that the group represents a monophyletic entity; however the question of how to classify the chemical variability exhibited within the group has remained unresolved. A phylogeny was inferred from ITS1, 5.8S, and ITS2 sequence data generated from a geographically and chemically broad sampling of populations within the L. neglecta group. While the inferred phylogeny recovered the core L. neglecta group as a strongly supported and monophyletic, the chemotypes within L. neglecta s.l. (i.e., the core-neglecta group excluding L. granulata) were not recovered as monophyletic and relationships within the group largely remain poorly resolved. Based on these results, a pragmatic circumscription for the group is proposed that emphasizes the strong correlation between morphological, ecological, and molecular characters over the lack of resolution between chemical and molecular characters. The names applied to members of the group are placed in synonymy with L. neglecta (these are L. alpina (basionym Crocynia alpina), L. alpina var. zeorinica, L. angardiana, L. borealis, L. caerulescens, L. caesioalba (basionym Crocynia caesioalba), L. caesioalba var. groenlandica, L. gelida, L. svalbardensis, and L. zonata). The results of these molecular phylogenetic analyses also 1) did not support the distinction of L. salazinica from L. elobata, thus that name is placed in synonymy here, and 2) elucidated the occurrence of L. humida in North America.