A phylogenetic analysis is presented, based on 57 morphological, anatomical, chemical and ecological characters, including 19 species from the genera Arthonia, Arthothelium and Syncesia. The aim of the study was to test the monophylyof some of the groups within the genus Arthonia suggested, for example, by Redinger (e.g. species with reddish ascomata, with grey-pruinose ascomata and with brown-black hypothecia). The results strongly support that Arthonia and Arthothelium are paraphyletic genera. The best-supported node contains all Arthonia species together with A. crozalsiana de Lesd., A. ruana A. Massal. (both hitherto placed in Arthothelium) and Syncesia myrticola (Fée) Tehler. A well-supported clade is formed by a group of pioneer species, often non-lichenized or poorly lichenized, including the type species of Arthonia, A. radiata. The species with reddish and/or K+ reddish ascomata form one clade and the species with more or less brownish or blackish hypothecia form another clade with Syncesia myrticola, the sister group to the Opegraphaceae and Roccellaceae. The results are discussed and compared with Redinger' grouping. Relationships to other genera within Arthoniaceae are briefly discussed. Arthothelium scandinavicumi Th. Fr., Arthonia dispersa (Schrad.) Nyl., A. punctiformis Ach. and A. mediella Nyl. are lectotypified.