The species-level taxonomy of the genus Graphis sensu Staiger was revised using numerical taxonomy and cladistic techniques. In its current circumscription, Graphis includes more than 300 species and is characterized by lirellae with well-developed, carbonized labia usually concealing the disc and usually hyaline, I+ blue-violet, transversely septate to muriform ascospores. The study analyzed the importance of morphological, anatomical, and chemical characters for taxonomic purposes in the genus, both at species level and at the level of species groups and lineages. A phenotype-based cladistic analysis, combined with a novel method to estimate the degree of character state homoplasies prior to a cladogram, as well as a species ordination using non-metric multidimensional scaling (NMS), was performed to assess the delimitation of potentially natural groups within the genus. Contrary to previous views, the most important character complex characterizing potentially natural groups in the genus Graphis is lirellae morphology, whereas labia striation, excipulum carbonization, ascospore features, and secondary chemistry, vary greatly even in closely related species. Based on these findings, Wirth and Hale's concept of ‘sporomorphs’ is emended to generally characterize morphologically similar species that differ in a single character, such as labia striation (‘labiomorph’), excipulum carbonization (‘excipulomorph’), hymenium inspersion (‘inspersomorph’), ascospore size and septation (‘sporomorph’) and secondary chemistry (‘chemomorph’).

A world-wide key to the genus Graphis is presented, based on extensive type studies and revision of several thousand historical and recent collections. A total of 330 species are accepted and included in the key, and a further 205 epithets are listed as synonyms. The structured key includes taxonomic information on type specimens of epithets considered to be synonyms of the accepted species. In addition, 28 species of other genera (Carbacanthographis, Diorygma, Dyplolabia, Glyphis) with carbonized excipulum and hyaline ascospores likely to be confused with Graphis are mentioned under the corresponding key couplets. Although the key is preliminary and some taxonomic and nomenclatural problems remain unresolved at this time, it should allow reliable identification of most specimens especially from tropical regions. The following 14 species are described as new: Graphis brahmanensis Aptroot sp. nov., G. cupei Vain. ex Lücking sp. nov., G. funilina Aptroot sp. nov., G. inspersolongula Aptroot sp. nov., G. leucaenae Aptroot sp. nov., G. lourdesina Aptroot sp. nov., G. myolensis Aptroot sp. nov., G. nadurina Aptroot sp. nov., G. norstictica Archer & Lücking sp. nov., G. sarawakensis Hale ex Lücking sp. nov., G. slendrae Hale ex Lücking sp. nov., G. subintermedians Hale ex Lücking sp. nov., G. subserpens Staiger sp. nov., and G. syzygii Aptroot sp. nov. In addition, 22 new combinations are proposed: Carbacanthographis cleitops (Fée) Lücking comb. nov., C. coccospora (Aptroot) Aptroot & Lücking comb. nov., C. induta (Müll. Arg.) Lücking comb. nov., C. triphoroides (M. Wirth & Hale) Lücking comb. nov., Graphis apoda (Zahlbr.) Lücking comb. et stat. nov., G. cremicolor (H. Magn.) Lücking & Archer comb. nov., G. enteroleuca (Ach.) Lücking comb. nov., G. evirescens (Redinger) Lücking comb. nov., G. galactoderma (Zahlbr.) Lücking comb. nov., G. ingarum (Vain.) Lücking comb. et stat. nov., G. isidiata (Hale) Lücking comb. nov., G. japonica (Müll. Arg.) A. W. Archer & Lücking comb. nov., G. kousyuensis (Horik. & M. Nakan.) Lücking comb. nov., G. negrosina (Vain.) Lücking comb. et stat. nov., G. oxyspora (Zahlbr.) Lücking comb. nov., G. plumbea (Zahlbr.) Lücking comb. nov., G. riopiedrensis (Fink) Lücking comb. nov., G. semirigida (Müll. Arg.) Lücking comb. nov., G. subradiata (Nyl.) Lücking comb. et stat. nov., G. subtecta (Nyl.) Lücking comb. et stat. nov., and G. sulphurella (Zahlbr.) Lücking comb. nov. Replacement names are established for six taxa: Graphis jeanmuelleri Lücking nom. nov. [≡ Graphina elegantula Müll. Arg., non Graphis elegantula Zahlbr.], Graphis neoelongata Lücking nom. nov. [≡ G. elongata Vain., non G. elongata Zenker], Graphis novopalmicola A. W. Archer & Lücking nom. nov. [≡ Graphina palmicola Müll. Arg., non Graphis palmicola Makhija & Adaw.], Graphis paralleloides Cáceres & Lücking nom. nov. [≡ G. rimulosa var. parallela Müll. Arg., non G. parallela Müll. Arg.], Graphis subalbostriata Lücking nom. nov. [≡ G. angustata var. albostriata Vain., non G. albostriata Vain.], and Graphis subvernicosa Lücking nom. nov. [≡ Opegrapha vernicosa Fée, non G. vernicosa Nyl.]. Three new synonyms are established for Glyphis substriatula (Nyl.) Staiger: Graphina sulcatula Müll. Arg., G. sulcatula var. conglomerata Müll. Arg., and G. bakeri Zahlbr.