While superficially resembling some members of the family Roccellaceae, such as Schismatomma and Mazosia, Synarthothelium differs in its ascus structure and larger spores.

The asci are clavate (club-shaped) to globose (roughly spherical), similar to those found in Arthothelium (referred to as Arthothelium-type), and contain large ascospores.

[3] Another genus in the Arthoniaceae with a thalline margin is Amazonomyces, but it is strictly leaf-dwelling (foliicolous), has differently shaped spores, and produces abundant reproductive structures with very large conidia.

[3] The genus Paradoxomyces, while sharing some features with Synarthothelium, lacks a thalline margin and is known only as a lichenicolous fungus (growing on other lichens) without its own visible thallus or associated algae.

[3] Synarthothelium was originally classified tentatively in the family Arthoniaceae[4] before being placed as incertae sedis (uncertain position) in the order Arthoniales in 2016, because of a lack of molecular sequence data.