Lichens of the Ramalina siliquosa complex dominate seashore cliffs in Europe and South-East Asia, but their taxonomy has been vigorously debated for over a century. On many cliffs, they exhibit a bewildering zonation of chemotypes that resembles the classic zonation of organisms that occupy the littoral zone below. Do the chemotypes represent separate species, or infraspecific variation? To better understand the systematics of this group, sequences from four genetic loci (ITS, IGS, RPB1 and RPB2) were obtained for 59 samples from Denmark, France, Iceland, Norway, UK, Japan and Korea, including all major chemotypes. Maximum likelihood analysis of these sequences, together with sequences from 36 other Ramalina species, reveals that the complex comprises two distinct phylogenetic lineages, each including multiple chemotypes. These two putative species-level lineages correspond to the currently accepted taxa R. cuspidata and R. siliquosa. There is no evidence that these two taxa are phylogenetic sister species. Consequently, the explanation of this chemotype complex as an example of ‘sibling speciation’ is rejected. Specimens traditionally called ‘R. siliquosa’ from South-East Asia form a third clade, identified here as R. semicuspidata, with an additional, divaricatic acid chemotype. Other results include a robustly supported clade of Ramalina species that produce medullary depsides and depsidones; this clade includes another well-supported clade of south-eastern United States coastal plain and tropical Ramalina species. By contrast, large, strap-shaped Ramalina species that lack medullary depsides and depsidones occur in separate lineages. In addition, close relationships between the following groups of species are indicated: R. farinacea with R. subfarinacea; R. fraxinea with R. leptocarpha, R. menziesii and R. subleptocarpha; R. sinensis with R. unifolia. Furthermore, a new, variolaric acid-only chemotype is reported for R. farinacea, and a new, acid-deficient chemotype is reported for a more broadly circumscribed R. culbersoniorum.

A key is given to the foliose and squamulose lichens known so far from Rondônia, including also corticolous crustose lichens with a chlorococcoid alga. The foliicolous Lecanorales found are also listed. The following four new corticolous Lecanorales are described from Rondônia: Calopadia granulosa with a granular, corticate thallus and ascospores 1 per ascus, 33–38×10·5–13·0 µm; Crustospathula amazonica with irregularly capitate to nearly globose, c. 0·2–0·4 mm diam. soralia on cartilaginous stalks; Flavoparmelia plicata with a thallus containing usnic and protocetraric acids, with laminal, irregular, globose to cylindrical isidia which are often easily abraded and showing the whitish medulla, but not sorediate or postulate; Physcidia striata with ascending squamules, without hypothallus, often with laminal isidia in defined areas towards lobe tips of some, usually sterile lobes, and often with biatorine apothecia with ascospores simple to 1-septate, (6·2–)7·5–10·0×(2·5–)3·0–3·5 µm. In the whole lichen flora of the lowland rainforest region of Rondônia, the following traits can be discerned: foliose lichens amount to only 17 species (2·7% of nearly 600), 33 (5·5%) are squamulose, while the vast majority (91·8%) are crustose. Cyanobacteria are present in only 6 (1%) species. A chlorococcoid alga present in c. 100 (16%), 12 of which (2%) have a myrmecioid alga. The remainder of the species, a staggering 83%, have trentepohlioid alga, including 6 (1%) with Phycopeltis. In neotropical lowland rainforest, the vast majority of the lichens are crustose and contain a trentepohlioid alga, and the Arthoniales, Graphidaceae and pyrenocarpous lichens are the main groups, each accounting for roughly a quarter of the lichen biodiversity.

Ramalina celastri is a highly variable, widely distributed pan-subtropical lichen species. In Australasia the species had been separated into two subspecies; R. celastri subsp. celastri and R. celastri subsp. ovalis. This study compares morphological variation, substratum preference and sequences of the internal transcribed spacer (ITS) and intergenic spacer (IGS) regions of ribosomal DNA from a range of specimens from New Zealand and one from Australia. Bayesian and ML trees generated using the sequence data form two well-supported clades corresponding to the two previously recognized subspecies. Molecular, morphological and geographical differences support the recognition of R. ovalis at the species rank.

The new species Bacidia termitophila, Coenogonium coppinsii, Fellhanera termitophila, and Micarea termitophila are described from termite nests in rainforest in Rondônia and adjacent Amazonas. Lichens were found on termite mounds on the ground but most of the species were also found on termite nests on trees. This substratum may serve as the most important locality for terricolous lichens in rainforests, and the natural habitat for species known mostly from road banks.

The lichen genus Biatora comprises inconspicuous crustose lichens that are typically found on organic substrata such as tree bark, bryophytes and detritus. During the last 20 years many new species have been added to the genus making its delimitation more and more difficult. The infrageneric relationships of the 42 species have never been investigated thoroughly. Using DNA sequences from three gene loci (ITS, RPB2, mrSSU) and 59 OTUs, an attempt was made to reconstruct the phylogenetic relationships of Biatora and its infrageneric groups. Cliostomum appears to be the closest relative of Biatora. The position of Mycobilimbia in the Lecania-clade is confirmed. Phylogenetic relationships within Biatora are poorly supported, but six different species groups that are also phenotypically distinguished are more or less well supported: the vernalis-, meiocarpa-, hertelii-, ocelliformis-, beckhausii- and rufidula- groups. The analysis also confirms the presence of several undescribed taxa. Biatora subduplex as currently circumscribed appears to be heterogeneous, as does B. helvola. Based on the phylogeny, the distributional range of B. alaskana is extended to Japan. The new combinations Biatora ementiens (Nyl.) Printzen and Biatora hemipolia (Nyl.) S. Ekman & Printzen are made and both names are typified.

A taxonomic and biogeographic overview of the genus Myrionora is provided. Two species are recognized, M. albidula (Willey) R. C. Harris and M. pseudocyphellariae (Etayo) S. Ekman & Palice comb. nov. The genus is characterized by polysporous asci, the presence of crystals in the hymenium and proper exciple that partly consist of lobaric acid, and a photobiont with large cells (mostly in the range 12–20 µm). Myrionora albidula is currently known from Germany, Norway, Sweden, the Russian Federation (Altayskiy Kray, Chelyabinskaya Oblast', Khabarovskiy Kray and Zabaykal'skiy Kray), and the United States (Alaska, Connecticut, Maine and Massachusetts). It inhabits bark of deciduous trees and shrubs and conifers over a wide range of latitudes. Myrionora pseudocyphellariae is known from Chile and Ecuador, where it has been encountered on lichens and decaying bark. Based on morphological characteristics, we conclude that Myrionora belongs in the Ramalinaceae.

Lecania chlorotiza and L. falcata, described here as new from Spain/Navarra, the Canary Islands and the Azores, do not belong to Lecania s. str. They belong to a strongly supported clade comprising Bacidia, Bacidina, Scutula and Toninia when examined with maximum parsimony, maximum likelihood and Bayesian inferences using mtSSU, nuLSU and nuITS sequences. This clade represents the Bacidiaceae and is included in the Ramalinaceae s. lat. Most genera included in that family need further work before a new genus can possibly be described for Lecania chlorotiza and L. falcata.

Bacidia rosellizans S. Ekman is described as new to science. Morphologically, the new species is similar to the type species of the genus, B. rosella (Pers.) De Not., particularly in the pale pink and pigment-deficient apothecia and in having the proper exciple and upper part of the hymenium inspersed with minute crystals that consist at least partly of atranorin. Bacidia rosellizans, however, differs in having a thin whitish thallus, smaller apothecia and a thinner apothecial margin, a dense layer of crystals along the excipular rim, shorter and narrower ascospores with fewer septa, and septate conidia. Whereas B. rosella is a species occurring in the nemoral zone of Europe and possibly northernmost Africa and parts of Asia (but not North America), B. rosellizans is found mainly on Populus and Salix in taiga. This species is currently known from Sweden, Russia, Canada and the USA. It was erroneously treated as Bacidia rosella in a monograph of North American corticolous species of Bacidia and Bacidina by Ekman (in Opera Botanica 127, 1996).

Australian records of Scoliciosporum are reviewed. The new species, Jarmania scoliciosporoides Kantvilas, is described, based on Tasmanian material previously referred to Scoliciosporum pruinosum (P. James) Vězda; the systematic position of these two taxa is considered. Two further species recorded previously, S. compactum Körber and S. umbrinum (Ach.) Arnold, are discussed and all records united under the latter name; S. umbrinum is reported from Tasmania for the first time.

The new species Megalaria allantoidea Fryday is described from the subantarctic Îles Kerguelen in the southern Indian Ocean, where it grows over terricolous bryophytes or Azorella selago cushions. It differs from all other described species of Megalaria in having large, sausage-shaped ascospores. The systematics of the genus Megalaria is reviewed, ascus structure of some previously described species revised, and the position of the new species in the genus discussed.

Bacidia coprodes (Körb.) Lettau, until now treated as a synonym of Bacidia trachona (Ach.) Lettau, is resurrected. Morphological, chemical and ecological characteristics place this species close to Toninia in the Ramalinaceae, but we retain it in Bacidia because of uncertainties in the generic taxonomy of this family. Bacidia coprodes is fairly widespread on calcareous and enriched siliceous rock in Europe and eastern North America. In North America the species has also been known under the synonyms Bacidia granosa (Tuck.) Zahlbr. (basionym: Lecidea granosa Tuck.) and Bacidia pammellii (Fink) Zahlbr. (basionym: Bilimbia pammellii Fink). Morphological and chemical features, together with molecular data, suggest that B. trachona does not belong to Bacidia, but rather in the Pilocarpaceae.

A new Mediterranean species, Waynea cretica, is described. The species is so far known only from Crete (Greece). Waynea cretica has flat to scarcely ascending squamules, an upper cortex being a paraplectenchymatous eucortex, and long, narrow, acicular ascospores with (5–)7 septa. The new taxon is compared with the hitherto known species of Waynea.

Bacidia pycnidiata sp. nov. (Ramalinaceae) is described from Poland and the Czech Republic. It is the first species within Bacidia s. lat., referable to the Bacidina group, known to have sessile, long-necked, lageniform pycnidia bearing straight macroconidia. It has been found growing on saxicolous as well as on corticolous bryophytes and directly on bark of deciduous trees within young, hardly changed woodlands or in the vicinity of human settlements.