Hypotrachyna is a speciose genus of primarily tropical and oceanic lichen-forming fungi. It includes species with distinct distribution patterns, such as pantropical, restricted and disjunct species. We used a dataset of mitochondrial SSU, nuclear ITS and LSU ribosomal DNA from 89 specimens to study the historical biogeography of the genus. We employed Bayesian and maximum likelihood approaches for phylogenetic analyses, a likelihood-based approach to ancestral area estimation, and a Bayesian approach to estimate divergence times of major lineages within the genus based on molecular evolutionary rates for ITS and a secondary calibration point at the Hypotrachyna clade – Parmeliopsis split. Our analyses suggest that the genus might have originated in the Neotropics during the Eocene and that the split of major lineages happened primarily during the Eocene and Oligocene. The major diversification within those clades is estimated to have occurred during the Miocene. Pantropical species distributions are explained by long-distance dispersal. A number of currently accepted species were found to be non-monophyletic, illustrating that the delimitation of species in the genus needs attention.

The new species, Mycocalicium llimonae, is described based on specimens collected from cones of Pinus halepensis in the west of the Iberian Peninsula. The new taxon is compared with the other species of the genus Mycocalicium in the Iberian Peninsula, particularly Mycocalicium subtile, and also with other genera in the Mycocaliciaceae.

ITS rDNA sequence data shows that Diploicia and Diplotomma species form a monophyletic clade distinct from other Buellia species. This indicates that Diplotomma merits acceptance as a genus, and suggests that Diploicia should be treated as a synonym of Diplotomma, the earlier name. The data also shows Diploicia subcanescens, considered the fertile counterpart in a species pair with D. canescens, is nested within D. canescens and should be treated as a synonym despite reported chemical differences. In addition, the molecular data support the distinctness of Diplotomma rivas-martinezii, a species restricted to gypsum rocks in Spain, from the widespread D. venustum, which grows on calcareous rocks. Aposymbiotic cultures suggest that D. rivas-martinezii also differs from D. venustum in its germination and isolation success rates. One new combination is made: Diplotomnta pulverulenta (Anzi) D. Hawksw. (syn. Abrothallus pulverulentus Anzi) for the lichenicolous species previously known as Buellia pulverulenta.