Taxonomic concepts of lichenicolous Arthonia species are presented. Species taxonomy is based on a range of 'new' and traditional characters. The potential of epifluorescence- and confocal laser scanning microscopy for the evaluation of new characters and a better circumscription of species is emphasized. Together with their lichenized relatives, more closely related lichenicolous Arthonia species are assigned to species groups with putative monophyletic origin. This offers a more natural classification scheme and serves as a base for a better understanding of the relationships of lichenicolous and lichen-forming taxa of the genus Arthonia. The lichenicolous species Arthonia japewiae, A. phaeophysciae, and A. sherparum are described as new. Taxonomic notes are given for Arthonia apotheciorum subsp. caerulescens and A. vagans var. lecanorina.