An identification key is presented for the accepted species of the lichen genera Anthracothecium (comprising 5 species) and Pyrenula (with 169 species, including 7 still undescribed). The key also contains some similar taxa and is complete for Blastodesmia (1 species), Sulcopyrenula (4 species), and Eopyrenula (6 species), but not for others such as Aptrootia, Architrypethelium, and Lithothelium, of which only the corticolous brown-spored taxa are treated. The following new combinations were found to be necessary: Anthracothecium interlatens (Nyl.) Aptroot, Pyrenula breutelii (Müll. Arg.) Aptroot, Pyrenula ceylonensis (Ajay Singh & Upreti) Aptroot, Pyrenula fusispora (Malme) Aptroot, Pyrenula gibberulosa (Vain.) Aptroot, Pyrenula lyoni (Zahlbr.) Aptroot, Pyrenula papillifera (Nyl.) Aptroot, Pyrenula platystoma (Müll. Arg.) Aptroot, Pyrenula schiffneri (Zahlbr.) Aptroot, Pyrenula welwitschii (Upreti & Ajay Singh) Aptroot, and Sulcopyrenula subglobosa (Riddle) Aptroot. Pyrenula sexluminata Aptroot is a new name for Pyrenula quinqueseptata Aptroot, and Pyrenula neosandwicensis Aptroot is a new name for Anthracothecium sandwicense Zahlbr. In addition, all known and many novel synonyms are cited, and the disposition of all other taxa in the two genera Anthracothecium (with 155 names) and Pyrenula (with 745 names) and their generic synonyms. Bogoriella was found to be an older name for Mycomicrothelia.